Larry Flynt has won. He was America's pioneer pornographer – the man who fought against a still-Puritan nation all the way to the Supreme Court for the right to get vaginal close-ups into the grasp of every young man. This fight got him jailed. It got him shot. It got him rich. And at the end of it, the grandchildren of the people who demanded his arrest for launching Hustler magazine think nothing of clicking on XTube to view a million women splayed a million ways, or uploading their own sex tapes onto the site for everyone to see. He is the founding father of our new pornucopia. His brand of hardcore porn is everywhere, leaking into every email inbox. For him, it's a story of freedom triumphant. But does Flynt's story also show the costs – and the casualties – of the Dionysian frenzy he has helped unleash?

He extended our freedom by encouraging people to chuckle and masturbate over scenes of the most horrific unfreedom – women being gang-raped, young girls being molested, "bitches" being shaved and slaughtered in concentration camps. One of his daughters says he molested her. Another of his daughters reportedly says he asked her to marry him. The cold Puritan morality of the Fifties badly needed to be relaxed – but in Larry Flynt, did it melt down into a moral Chernobyl?

These are the thoughts that were flickering through my mind as I waited in the lobby of the Four Seasons Hotel in San Francisco to meet Flynt. I had been scheduled to interview him several times before, but each time it was cancelled at the last minute for mysterious reasons. So when he is suddenly rolled towards me in his $85,000 golden wheelchair, it seems impossible that this man can bear the weight of these questions. In the videos of his from the peak of his fame, he is a red-faced eruption of testosterone, screaming at the camera in long Charlie Sheen-style soliloquies of inspired abuse. Now he is lolling almost lifelessly in a chair. His head is barely able to look up at mine, and his hand is barely able to reach up to shake mine.

He speaks in a very slow, strangulated gargle. "He-ll-o," he says. "You look –" gasp, long inhalation of breath – "about nine years old." I smile. He doesn't. He is 69, but looks at once much older and much younger. His face is round and entirely unlined, making him appear to be a gigantic, gnarled baby.

"Mr Flynt will speak to you upstairs, in a conference room," says the huge Italian-American man with a tiny pencil moustache who is pushing his wheelchair. "Not here." I later discover this man – who looks like one of the minor cops on NYPD Blue – is called Frank Torres, and describes himself as Flynt's "bodyguard". He wheels Flynt into an elevator, and we stand there in silence. Flynt's head rolls about, as if unsupported. Frank takes out a comb and brushes Flynt's hair, and when he is finished, Frank says: "Thank you, sir."

In the conference room, I ask Flynt how he is. "Lousy," he says. I have to lean in and listen carefully: his voice is gargling and hard to decipher. "I've been on this book tour and you travel all over the place. I don't know how those businessmen do it – Singapore one day, London the next. They must get good hookers." Frank pours him coffee, and says "Thank you, sir" again. He whispers something in Flynt's ear and then steps outside. He leaves the door ajar and peers through, listening the whole time.

Flynt's story begins in the poorest county in America. The town of Lakeville, in the hills of Eastern Kentucky, had forty residents, comprised of five families. They lived isolated along dirt roads. No asphalt was laid until Flynt was 10, in 1952. "It was like a medieval settlement," he says. Most of the people there were illiterate, and hadn't travelled more than a few miles in their entire lives. His father found it so agonisingly boring he was almost constantly drunk, and would vanish on booze-benders that lasted for months. One time, when he was an adolescent, Larry was so enraged by this he smashed his dad in the face with a whisky bottle, and thought he'd killed him.

His father claimed Flynt's mother, Edie, as his wife-to-be when she was just 14. That must, I say, have been hard for her. "Ah," Flynt says, shrugging. "Not necessarily. Where I'm from, people got married very young. That wasn't a difficulty." Really? It didn't harm her to be sexualised and married off so young? "No. I don't think so. Not at all." His daughter, Tonya, says Flynt feels "great anger" towards his mother, who had a reputation in the town for sleeping around, and that he regarded her as "a whore". So I ask Flynt if he remembers when he first found out his mother – who worked three menial jobs, one after the other – was promiscuous. He looks vacantly, away from me, for such a long time that I think he might not have heard me. Then says: "I don't think when any child finds that out about his mother it's pleasant. It's disturbing. But you've got to go on. You've got to live with it. I don't mean to interrupt you, but did you read the book? Did you get a copy?" He wants to talk about his new book – which we will discuss later. I want to know about the life.

Flynt believes his different attitude to sex was born in those hills. "I'm a hillbilly and people like me come to sex without all the hang-ups imposed by the hypocritical morality of the middle class," he once wrote. Yet his autobiography, An Unseemly Man, contains many passages that present children in strange ways. His first sexual experience, he says, was when he was seven. He says his cousin, another seven-year-old, asked him to "do it" with her and "I did a lot of squirming and humping as she instructed". He says about his first wife, Peggy: "Her mother had let her screw around since she was 10 years old." I ask if she really wanted to. "It was different times," he says, shrugging.

He lost his own virginity at the age of nine, to a chicken. He describes penetrating its egg sack, and how "when I let the chicken go, it started towards the main house, staggering, squawking and bleeding" – so he immediately killed it. Did you feel bad for the chicken? "What? No. It was a" – long breath, gasp – "chicken."

And then he was molested himself. When he ran away at the age of 15, he was picked up on the side of the road by a man and forced at gunpoint to take part in sexual acts. How did this affect you? "I don't think it did. I've always been heterosexual. I've never had thoughts of being gay." But abuse isn't about sex for the victim, I say. He looks puzzled by this. "It made me more aware," he says. Of what it's like to be a victim of sexual assault? "No." He looks bemused by the question. "Of... uh.... It didn't cause any psychological trauma."

As a young man, he charged around aimlessly, "nagged by an inferiority complex", hemorrhaging rage. He got married very young to a woman he quickly hated, and when her mother objected to how he treated her, Flynt shot at her. He missed, but only avoided jail by pleading insanity. He was put in a psychiatric unit and given electroshock "treatment" until "I didn't know who I was". He wrote a letter soon after saying: "I am the evil product of an evil soul." He says he can't remember a lot of this period, because "I've spent most of my life hyped-up, doped-up, or drunk".

But he can still remember the birth of Hustler. Flynt set up a series of strip clubs, where he bragged: "I'm selling pussy by the glass." He was taking amphetamines the whole time and was sexually "insatiable, sometimes having sex with a different woman every four or five hours". Then, in 1974, he decided to publish a magazine to be distributed in his clubs. He thought he had spotted a gap in the market. Playboy was serving up "sanitised, idealised women", and focused on their breasts and legs. "I was always interested in the crotch," he says. "And [in] real women... I dared to portray people's real sexual fantasies, not somebody's idea of what fantasies should be." That was his secret, along with – as he put it in his autobiography – "showing a very young woman with an older man". (All of Hustler's models, he later adds, have always been over the age of 18.)

He has a script he wants to slowly recite about his life story, which he offers haltingly, like an ancient text that has only been partially recovered. It has some good lines in it – "Moses freed the Jews. Lincoln freed the slaves. I freed the neurotics" – but I've heard them a hundred times. Whenever I interrupt his recitation with an unexpected question, his face flickers a little, and he looks confused.

So I let him go back to his text for now. He is telling me about his famous court cases. He spent years going from one court case to another, in any state that claimed Hustler was "obscene" – and he was constantly under threat of being sent to prison for it. "At my first court trial I was [initially] sentenced to 25 years in prison without bail," he says. "That's when the fight for free speech began. It never stopped because there was always some prosecutor somewhere in the country who wanted a piece of me and I was always there to oblige them... I remember we had a case in Nashville, Tennessee. It was a jury entirely of women, all aged 60 or over. It took them 20 minutes to acquit. I knew then that something was changing in America. They might not want to see it but they didn't want the government telling them what they can and can't see."

His most famous case was against the Christian fundamentalist preacher Jerry Falwell. Hustler ran a mock interview with Falwell, in which he lovingly described his first sexual experience – in an outhouse, with his own mother. The case went all the way to the Supreme Court. Appearing before the Justices, Flynt screamed that they were "eight assholes and a token cunt" – only for them to find in his favour.

Then, one morning in 1978, Flynt's ripple of legal victories was suddenly halted on the doorsteps of a courthouse in Georgia. He was walking into court when he heard a loud crack – and looked down to see "my intestines were spilling out of my body. The front of my stomach had been ripped off". He had 11 surgeries, removing six feet of his intestines. "It felt as though I had been disemboweled and hung on a meat hook in my grandpa's smokehouse," he says. Nobody was ever arrested, but eventually a white supremacist called Joseph Paul Franklin claimed he had done it because he was outraged by an interracial photoshoot in Hustler. Flynt says: "He killed about 25 people, but when he was asked by an interviewer if he regretted any of it, he said, 'Yeah. I hear Larry Flynt is a really nice guy. I shouldn't have shot him'." He laughs, and then his laugh seems to run away from him uncontrollably, and suddenly his face reverts to its blankness, and his head lolls forward.

He never walked again. He says he can still function sexually "with a battery device" – I don't ask the details – but for a man who seems to have a volcano of pure libido, it must have been agony. Larry Flynt unable to get an erection, I say to him, must have been like Picasso with his hands cut off. "It hasn't caused me so many problems," he says. "I resolved early on not to think about something I can't change." And he looks away. I am trying to think of a polite way to ask what, physically, has happened to his body in the past few years, and why he seems so slow. He says: "I'm like – you know, there's a phrase, about a racehorse that's run too many races and been beat too much. I been in a lot of prisons, I got shot, I took a lot of drugs. I'm beat."

Flynt can make a rousing Voltairean case for freedom of speech, and for his place as a martyr in its cause. He has plenty of practiced lines about the people who oppose it, many of them funny: "The right-wing of the Republican party isn't so much a political agenda as a plea for help," he says.

I try to explain that I absolutely support his right to free speech – but find the way he has chosen to use his free speech in Hustler despicable. I describe some of Hustler's most notorious photoshoots to him. "Dirty Pool" depicted a woman being gang-raped on a pool table. A few months after it was published, a woman was gang-raped on a pool table in a town called New Bedford – and Hustler responded to the criticism suggesting they may have inspired the assault by publishing postcards of another woman being gang-raped on a pool table with the greeting: "Greetings from New Bedford, Gang Rape Capital of America."

Then I describe "The Naked and the Dead", a Hustler spread in which a woman is forcibly shaved, raped, and apparently killed in a concentration camp. Who, I ask, finds that sexy? "That is satire. That's what I went to the United States supreme court for. It was a landmark judgment. It was a unanimous decision. Supreme Court Justice William Rehnquist, one of the most conservative justices, said sometimes things are done under the name of the First Amendment that are less than admirable but that doesn't give the government the right to suppress it."

I'm not arguing it should be suppressed, I explain. I support your right to say it – just as I have a right to respond by saying it's vile and asking you why you did it. "It's satire," he says, testily. But what's it satirising? "What?" he says. What's it satirising? "It's satirising the whole idea of a pretty girl being executed." But how is that a concept that needs satirising? How is that even a concept at all? "It wasn't done as any kind of statement," he says. But you just said it was a statement – a satirical one. "There wasn't any malice in it," he says. Really? It's a non-malicious concentration camp?

Suddenly, Frank appears from behind me. "More coffee, sir?" he says to Flynt, whose cup of coffee is still full. He doesn't look at me at all. Frank takes away Flynt's old coffee and pours out a new cup, says "Thank you, sir" once again, and then returns to his spot just outside the door.

I think back to the pictures from Hustler of women with rats coming out of their vaginas. Don't you think this suggests a deep hatred of women's sexuality, probably stretching back to your rage at your mother? He doesn't react. His face registers nothing. "No," he says eventually. I wait for him to say more, but he doesn't.

You say that Hustler is all about dissolving sexual shame – but, in fact, your pornography feeds on shame. It is the lifeblood of Hustler. "Look," he says, "you're talking to me about something that is legally protected speech and I don't feel I have to explain the various parodies and satires we do in the magazine. I will concede to you one thing – Hustler is offensive, even to the point of being iconoclastic. That's our purpose – to be offensive. We're always pushing the envelope, it's understandable that people are getting upset – but that's what built our reputation and it's what our core readership like."

These shoots he refuses to defend seem to embody the contradictions of the porn age – there's greater sexual freedom for some, and a greater celebration of sexual violence against others. I decide to read him an open letter that a feminist group, The Praying Mantis Brigade, wrote to him in 1981. They said: "You routinely make a laughing matter out of sexual torture. How do you think the victims of the Hillside Strangler feel reading Hustler's parody glorifying him? Larry Flynt you were the victim of a violent, lawless act. Did you love the brutality directed against you in 1978 in front of the Georgia courthouse? Did you find it sexually exciting? If not, why do you continue to perpetuate the myth that women enjoy suffering pain inflicted by sexual violence?"

He looks puzzled. "Wha-at?" At times, this interview feels like I am yelling questions into an empty cave, and hearing only a distant echo come back at me. I read it to him again. He seems to wheeze a little. "I don't get it. What are they saying? What does she mean I didn't enjoy it? What happened to me?" You were shot by a lunatic. "That wasn't a sexual act. So how can you compare it?" But being gang-raped isn't a sexual act for the victim. Being put in a concentration camp isn't a sexual act for the victim. Being killed by the Hillside Strangler wasn't a sexual act for the victim. That's the whole point. He interrupts me and says – speaking fast for the first and only time in the interview – "I don't even remember if we did something on the Hillside Strangler, but if we did, what's that got to do with me being shot?"

Many of the images that have made you rich imply women enjoy being sexually assaulted and killed. You have been sexually assaulted and you have been nearly killed, and you didn't enjoy it. Do you see any connection? "I don't know how many different ways I can say this – the First Amendment gives me the right to be offensive. If you're not going to offend somebody you don't need the First Amendment. I don't have time to deal with the impulses of people who can't control themselves... I am in the casino business [he owns a chain of them] and all the time we get people saying we have to help problem gamblers. I say – why? I don't have time to deal with people's problems." Then he says, with what seems to be genuine bewilderment: "I don't know why you're asking these questions."

The most serious (and most fiercely contested) charge against Flynt – politely ignored by the supposed liberals who queue up to champion him as an icon of freedom – is worse still. It is that he was a child molester. I decide to raise the topic sideways at first. I ask about a comic strip he ran in Hustler for 13 years, called "Chester The Molester". It featured an old man who, in each strip, would trick prepubescent or adolescent girls into pleasuring him. A typical cartoon shows a little girl in a hiked-up dress hurtling down a playground slide, while Chester the Molester is waiting at the bottom with his tongue hanging out. The man who drew the cartoon, Dwaine Tinsley, was convicted of raping his own daughter, Alison, and of forcing her to take birth control pills from her 13th birthday onwards. He served two years in prison – and Hustler continued to publish the cartoons drawn from his jail cell.

Flynt looks irritated. "Dwaine Tinsley was a genius," he says. "He was at one time in America in the Seventies and Eighties the most brilliant and recognised cartoonist in America... I liked him. He was an old country boy, you know." What would you say to his daughter about why you employed him? "He was released." Yes, on a technicality – not because he was innocent. "I never got involved in that because I never knew what the circumstances were so I don't really have a comment on them. It doesn't at all reconcile with the person I knew." Really? It seems jarring to you that a man who drew a cartoon lauding child molestation was actually a child molester? "I don't know. It may very well have happened. I wasn't involved." Doesn't that suggest a very casual attitude towards the rape of children? That you're not bothered by it? That you would publish a cartoon joking about child molestation by a child molester in his prison cell? "Wh-at? No. Paedophiliacs don't read Hustler. Hustler is an adult thing."

Flynt's daughter, Tonya, claims she remembers those cartoons very well. In her memoir, Hustled, she alleges that her father showed her those cartoons when she was nine and "began to explain what little girls do with their fathers... The cartoon character with the erection represented the good, loving father. Dad's hand moved to my breasts". She says the molestation made her "filled with self-hate, anxious to be done with life as I know it, even if death was the only way out".

When I read this passage to him, Flynt's face doesn't move. He looks limp, and impassive. "You know she waited until she was 40 years old to say that I molested her when she was 10," he says. "When I asked her why she didn't come forward sooner, she said it was that – what do you call that memory thing? The memory thing. The authorities never took any action because they didn't believe she was credible. I know what it's like to be falsely accused. These women are always vying for attention. They [Tonya, and her sister] were living with their mother. I didn't get on with their mother at all so I didn't have any relationship with them. I remember when she was in high school she called me and said" – he adopts a mocking, whiny little girl's voice – "'Why are you out to screw my life up? Everybody at my school knows your job. I'm ashamed of my name. Blah, blah, blah.' And I said – I got a solution for ya. For ten bucks go to the local courthouse and change your name."

He continues: "She got a deal where she was speaking at these churches around the country and they'd pay her four or five hundred dollars to speak and say what a horrible father I was." (In interviews, Tonya denied this was her motivation.) "I just ignored her until finally one day she contacts me and says, 'I don't know why I said the things I said'. That was the last conversation I ever had with her. I think really she was looking for attention because I divorced her mother when she was very young – maybe a couple of years old. In her whole lifetime I saw her maybe three times." (I haven't been able to track down Tonya to ask if this is true.)

She isn't the only one of your children who it has been alleged you abused, I point out. According to the journalist Matt Labash in the Weekly Standard, your daughter Judy says you asked her to marry you when she was 20. According to a recording that Penthouse magazine claims is of your voice, you inspected the naked body of your 13-year old daughter Theresa "to see if you were built like your mother". (Theresa says she "vaguely remembers something about a tape" but denies she was abused in any way.) Flynt lets out a long sigh. "This is all bullshit," he says. "I never touched anybody, I swear to you I never touched anybody. My daughter Theresa works with me in my company. She's the only one of my children who was smart enough to go and got an education and we're incredibly close. It's bullshit. You ask her, they made it up, because [they are] Republicans and I expose Republicans, [or because] Penthouse are rivals [to Hustler]. I wanna talk about the book now."

Oh. Yes. The book. Flynt has co-authored a book called One Nation Under Sex, which traces the sex lives of America's Presidents from its founding. It shows how the US has had a President who at the age of 43 had sex with a 14-year-old slave-girl (Thomas Jefferson), a gay President (James Buchanan), and – this is his "favourite story", he says – a First Lady who was only 19. "Grover Cleveland's wife died on the campaign, so he married the nanny. Today, you'd get called a cradle-snatcher for that," he says, and lets out a gurgling chuckle. So soon after we had been arguing about child molestation, this chuckle seems to hang in the air. I am silent. I don't think he notices.

It's hard to keep him focused on this subject, or any subject. His conversation skids about. He doubts Barack Obama would cheat on his wife because: "You ever looked at her? If he ever cheated on her she'd kick his ass. You know they may be black but they've got a very stable family." Then he says, apropos of nothing: "Sarah Palin is the dumbest thing. But I made a fortune off of her. [He made a porn film called Nailin' Palin, based on her]... She did a disservice to every woman in America. She knew from the first month of pregnancy that kid was going to be Down's Syndrome. It's brain dead. A virtual vegetable. She carries it to all these different political events against abortion, she did it just because she didn't want to say she'd had an abortion. How long is it going to live? Another 12, 15 years? Doesn't even know it's in this world. So what kind of compassionate conservative is she? I don't think anybody will want her near the White House." I am so thrown by the unpleasantness of all this I don't even interject.

There have been moments in Flynt's life when it seemed that he had sudden jolts of self-awareness. In 1977, he had some kind of mental breakdown and began having startling hallucinations where he thought St Paul and the late comedian Lenny Bruce were talking to him. At that time, he announced publicly: "I owe every mother an apology for treating women like pieces of meat." When I read him this quote now, and ask if there was any truth in it, he says it was "a psychotic or manic depressive episode. It's not how I think. I've been on medication since then and I've never had thoughts like that since". But what if you were right then? He looks down. "I wanna talk about the book."

Do you think, Larry, you have written this book showing all of America's leading figures were sexually dysfunctional to make your own dysfunction seem normal? Just as I ask this, Frank appears again. "The photographer is ready for you now," he says, very firmly. Flynt looks at me and says, out of nowhere: "Pornography is a release mechanism and a lot of men use it to masturbate to. It's better than going and killing some hooker in a dark alley." He adds: "I don't know how you can write a decent article with the questions you've asked." Then, in a lower voice, rather like the whiny one he used when mocking his daughter: "You're going to take the feminist side." And with that, Frank wheels him away.

I watch while he is photographed downstairs, in the hotel's restaurant. The snapper asks Flynt to keep his gaze focused on a particular spot – the camera lens, or an object in the room – but it seems like he can't focus for more than a few seconds. His eyes roll away, aimlessly, and then he looks lost. "Look at me, sir," Frank eventually says, and it seems that he can keep his eyes on Frank for slightly longer, but then he loses his focus again. I'm not sure what has happened to him, or why. But as I watch this, I realise where I have seen that pained, slightly panicked blankness before. It is the look on the face of all the Hustler "models" in all the shoots across all the years.

One Nation Under Sex: How the Private Lives of Presidents, First Ladies and Their Lovers Changed the Course of American History by Larry Flynt and David Eisenbach, published by Macmillan Books.