My family went into central London last week. After they'd gone, I found myself checking the web for reports of bomb blasts. Absurd and paranoid of me, of course. Rationally, I know that a motorist is more likely to kill you than a terrorist. Ever since Iraq, I have also known that the intelligence services' "threats" can be imaginary. But I know this, too, and so does everyone else: if a bomb explodes, no one will think that a "militant atheist" has attacked his or her country. No one will mutter: "I wonder if someone has taken this god delusion argument too far." Or: "Atheists should have known that violent words lead to violent deeds."

The police don't send undercover agents into sceptic societies and parliament doesn't pass emergency laws to combat atheist violence. Fanatics threaten European Muslims if they abandon their faith but no atheist will attack them if they keep it. No one thinks that atheists threaten the lives of their fellow citizens anywhere in the west.

And yet across what passes for the intelligentsia, moral equivalence holds sway. There is militant religion on one side and militant atheism on the other. We've no obligation to make a choice between them. Indeed, we should devote our energies to attacking atheism rather than religion. You'd never guess it from the way believers and conventional intellectuals throw the term around, but "militant atheism" has a specific meaning. Marxist-Leninists, who persecuted all faiths whenever they assumed dictatorial power, were authentic militants. If you want to see militant atheism today, look at China, which sends supporters of Falun Gong to its black jails and bulldozes Catholic churches.

If you were foolish enough to take the west's religious apologists at their word, you'd think that atheists were proposing the same pogroms here. Their victimhood takes two malign forms. First and most prominently, the Christian right is rallying opposition to equality with the cry that the "intolerance of aggressive secularism", in the words of the communities secretary, Eric Pickles, is threatening faith. You get a taste of the hysteria on the right when you discover that the cause of the anger was a court ruling that a local council could not include Church of England prayers in its formal meetings. (As a public body, it had to respect the views of councillors and voters of other faiths or none.)

To a large element in modern conservatism, equal treatment for all is nothing less than the "aggressive intolerance" of Christianity, as is the legal requirement that hotel owners cannot ban gay couples from their rooms just as landlords once banned blacks, dogs and Irish from theirs. Do not underestimate the danger of their wails. One day, they could encourage a future Conservative government to repeal the Human Rights Act.

An intellectual climate, which is so pervasive that you can be forgiven for not noticing its strangeness, reinforces the persecution complex. Across left and right, in the BBC, academia and the supposedly serious press, atheism and "aggressive secularism" are attacked as a matter of course. When they are at their crudest, intellectuals (and I am using that term crudely too) uphold moral equivalence by claiming that atheists and humanists mirror the behaviour of religious believers. As atheists have nothing in common beyond an inability to believe in a god or an assortment of gods, the argument comes down to a critique of the minority of atheists who decided that, what with 9/11, Hindu nationalism and genuinely militant strains of Christianity and Judaism, the times required us to dispense with politeness.

The occasional dogmatism that followed apparently makes atheism "like a religion". It's not a charge I'd throw around if I were seeking to defend faith. When people say of dozens of political and cultural movements from monetarism to Marxism that their followers treat their cause "like a religion", they never mean it as a compliment. They mean that dumb obedience to higher authority and an obstinate attachment to dogma mark its adherents.

Meanwhile, I'm losing count of and patience with the apologists who tell me there would be no morality without religion. The failure of the serious press and BBC to question this is as shocking as it is depressing. We are almost 150 years on from the moment in 1867 when Matthew Arnold heard the sea of faith's "melancholy, long, withdrawing roar" on Dover Beach. Are religious writers suggesting mid-Victorian Britain was a more moral country in its treatment of women, homosexuals and the poor?

Few dare maintain that immorality has increased as religious observance has collapsed. Instead, they say that everyone's morality, whether they are religious or not, is rooted in our common Christian culture, or our common Judaeo-Christian culture or, as an opponent in debate told me last year, our common Judaeo-Christian-Islamic culture. Forget if you can that there is much in religious culture that is immoral, not least a willingness to slaughter each other, and consider that if everyone is religious then no one is religious; religion is emptied of meaning and just becomes a vague cultural inheritance, like driving on the left or letting off fireworks on bonfire night.

The bad faith of religious apologists is best seen in their theological emptiness. Scour their writings and you'll be hard pressed to find the one honest argument true believers from earlier ages would have recognised: you must reject atheism to save your soul. In my experience of intellectual London, those who shout loudest against militant atheism do not believe themselves. Faith isn't for our sort. We need it to discipline the lower orders and keep the natives happy.

Since 9/11, western intellectuals have had a choice. They could have taken on militant religion, exposed its texts, decried its doctrines and found arguments to persuade young British men not to go to Syria and slaughter "heretics". But religious fanatics might have retaliated. Instead, they chose the safe option of attacking the phantom menace of militant atheists, who would never harm them. Leaving all philosophical and moral objections aside, they have been the most awful cowards.