One evening in 2006, at a colleague's house, I met a friend of her teenage daughter. He was intellectually curious, and obviously bright - but implacably loyal to his parents' born again Christian faith. We spent pretty much the whole evening arguing with the poor boy, appealing to his logic and reason - all to no effect. There must, we despaired, be some seminal atheist text we could refer him to. We just couldn't think of one.

But lo - ask, and ye shall receive. Not a month later, Richard Dawkins published The God Delusion, a scorching manifesto for secularism. Even by the standards of Dawkins' 1976 bestseller, The Selfish Gene, it was a spectacular success, with sales exceeding 1.5m.

This week, as Dawkins retires from the Charles Simonyi professorship for the public understanding of science, the Oxford post he has held for 12 years, you might expect him to feel that the secular, scientific cause to which he has devoted his career is winning. On Tuesday, campaigners announced plans for an atheist advertising campaign to appear on the side of buses with the message: "There is probably no God. Now stop worrying and enjoy your life." The campaign, which was launched by TV comedy writer Ariane Sherine, blogging on Commentisfree.co.uk, hoped to raise £5,500 from supporters, which Dawkins had pledged to match with his own money, but by yesterday public donations had already raised more than £96,000.

In the same week, immigration minister, Phil Woolas, predicted that constitutional reforms would banish bishops from the House of Lords within the next 50 years, and record numbers of new maths and science undergraduates were reported. Even in America, the religious right seemed to be losing its grip.

But when I ask Dawkins, now 67, if he feels that public understanding of science has improved during his career, he looks doubtful. "I would say that when my academic career began there was probably just as much ignorance - but less active opposition [to science]. If you were to actually travel around schools and universities and listen in on lectures about evolution you might find a fairly substantial fraction of young people, without knowing what it is they disapprove of, think they disapprove of it, because they've been brought up to."

Does he attribute that to lower standards of scientific education, or to the rise of religious fundamentalism? "Oh," he says without hesitation, "I think it's due to greater religious influence."

In Dawkins' view, there is a battle taking place in Britain between the forces of reason, and religious fundamentalism and it is far from won. He is one of its most famous and prolific combatants - but the question might be whether he is among its most effective. The God Delusion's stated aim was to "convert" readers to atheism - but he admits that as a proselytising tool it has broadly failed. "Yes," he smiles. "I think that was a bit unrealistic. A worthwhile aim, but unrealistic."

In fact, Dawkins has been described as "the biggest recruiter for creationism in this country". Critics accuse him of an imaginative failure when it comes to human nature's susceptibility to the comfort of irrational thought. They say his intellectual intolerance alienates people, and have questioned his wisdom in attacking a target such as the comedian Peter Kay, for admitting to finding faith comforting. "How can you take seriously," Dawkins notoriously scorned, "someone who likes to believe something because he finds it 'comforting'?"

When Sherine approached him about funding for the atheist bus, the wording he preferred for the advert was "There is almost certainly no God". Wouldn't this just infuriate believers, and put off potentially sympathetic agnostics? In the end they agreed on "probably".

"Yes, yes, I know," Dawkins interrupts. "I know. People say I'm shrill and strident."

Dawkins has a theory about this, which is very persuasive. "We've all been brought up with the view that religion has some kind of special privileged status. You're not allowed to criticise it. And therefore, if you offer even a fairly mild criticism, it really does sound strident, because it violates this expectation that religion is out of bounds."

But even so, from a purely strategic point of view, why doesn't he therefore take more care to be ...

"Conciliatory?"

Well, yes. If people find the certainties of his intellectual style off-putting, why doesn't he try and make himself seem a little less intimidating

"Well, this is a thing that worries me," he says earnestly. "Yes. And I meet it all the time. And it's by far the most intelligent criticism that I meet. I suppose there are two different ways of doing it, and I'm extremely happy if other people do it that way. Dan Dennett's Breaking The Spell at least sets out to do that, to be seductive - is that the word? Not quite, but to seduce the reader in. And I can do that. I know how to do it." He pauses to reflect. "But I seem - I seem to have lost patience."

In actual fact, though, he does take enormous care throughout the interview to be patient. Although he regards it as "clearly wicked" to call the child of Catholic parents "a Catholic child", he quickly adds, "it's equally wicked to say this is an atheist child. I would never say that." He can't help adding, "Of course, some people would say all babies are atheist, because they don't believe in anything." But when I ask if he'd say that, he considers for a moment before replying, "Well, I'm not sure that's a very sensible way of putting it actually."

Does he worry that the calibre of undergraduates is falling, as access to university is extended? "I've got to be terribly careful not to sound like an old fogey here. When I first started tutoring in the 1960s it was a great joy to me, to get enthusiastic pupils who were really keen and interested and a tutorial would be a real meeting of minds and a real conversation. That good feeling about it seemed to gradually disappear. But I would hesitate to blame the students for that, it could be that I was just growing jaded."

Like most rationalists, Dawkins tends to invoke people's innate intelligence, and attribute their flawed ways of thinking to ignorance rather than stupidity. "But I don't have any evidence," he concedes. "I could be wrong. It's a kind of ideal. It's a sort of bending over backwards." People might just be stupid, I suggest. "They might be, yes," he agrees cautiously. "But at least my saying that ignorance is no crime is my defence against the charge of arrogance. Because if you tell people they're stupid, that certainly isn't the way to win friends and influence people."

Dawkins once described the British Airways employee dismissed for wearing a gold cross to work as having "the stupidest face". Did he regret saying it? A slightly naughty smile flickers over his face.

"Well ... well ... yes, I do really. Yes. That was an unguarded moment. Although I think I said stupid-looking. Did you see the photograph of her? I think if you look up the story, and they've got the photograph ... " He checks himself, and stops. "But this is unkind."

Before meeting Dawkins, I'd worried that he might be so intellectually impatient as to be crushing. The impression instead is more like that of a lion who has given himself strict instructions to behave like a pussy cat - which is both a relief, and just slightly disappointing.

Does he ever, I ask, envy people who believe in God?

"No." He shakes his head firmly. Even though faith is said to be so famously comforting?

"You see," he says, "I'm so eager to say well maybe it is comforting but so what? I suspect that for every person who is comforted by it, there will be somebody else who is in mortal fear of it." Does he not envy those who manage not to find God mortally fearful?

"If I envied them that, then I'd have to envy people who are on some drug, which just makes them feel good. So to the extent that religion's comforting, it's probably not ..."

Dawkins likes to joke that old people go to church because they're "cramming for the final". He never worries that one day in old age he may wake and find himself feeling drawn towards faith, though. If he did, he would put it down to senile dementia. He seems much more worried about spurious reports of a fictitious deathbed conversion being put about by his enemies after he dies. He is probably not joking at all when he says "I want to make damn sure there's a tape recorder running for my last words."