A television programme has just been cancelled after a militant group vowed to kill the woman whose opinions are central to it, because they disagree with her.

This has happened not in the Middle East or the United States, but here in Britain. Another, connected, militant group has forced British hospitals not to perform certain types of medical procedure of which it disapproves, by threatening doctors, nurses and patients with violence. It has also made threats to the staff of a small charity about accepting money from a source the militants consider tainted. The charity, fearful of its staff having to run the gauntlet of screaming protesters as they arrive at work, has turned down a desperately needed £3,000. The same group has circulated the telephone numbers of media people of whom it disapproves, and its supporters have telephoned to make death threats.

On college campuses in London and Manchester, lesbian and gay students have suffered harassment and menaces, and posters advertising gay meetings have been torn down and defaced. Gay activists have received death threats.

Another group has embarked on an organised campaign to destroy and deface hundreds of advertisements of which it disapproves. Yet another related group has recently forced a leading regional theatre to stop showing a play, by acting violently towards audiences as they went into the theatre, and throwing stones. Some of these events have been reported, but none has provoked the outrage one might have expected. The reason is that these groups are not made up of anti-war campaigners, or pro-Palestinians, or any of the usual suspects. They are all religious groups, and their thuggish behaviour has been treated with respect and understanding.

The television programme, previously unreported, was one of a series planned by the New Statesman's former deputy editor Cristina Odone, and it was to have explored why people leave the faith in which they were brought up. It was to feature a woman raised as a Muslim, explaining why she left. Militant Muslims vowed to kill her, and she knows she has to take them seriously - they murdered a friend of hers, the Dutch film-maker Theo van Gogh.

Coincidentally, it was Odone who first alerted us in these pages to what is going on. "Between conservative Catholics, the expanding Christian community and growing numbers of evangelical Protestants, an alliance is being forged," she wrote in November last year. "Its aim is to protect a faith-based value system against the encroaching secularism of the west."

Muslim groups are also responsible for attacks on gay people, according to the gay activist Peter Tatchell. Some gay students and lecturers are so worried about assaults from Islamist groups that they have ceased to be open about their homosexuality. Tatchell himself has had several death threats from Christian fundamentalists quoting Leviticus 20:13, which says homosexuals "shall surely be put to death". Muslims are also responsible for defacing advertisements: they consider the perfectly legal posters for such shows as Desperate Housewives to be improper.

It was a group called Christian Voice which taunted doctors, nurses and patients, pledging to harm them physically if they carried out entirely legal abortions. Members of the group block patients' paths as they try to enter the hospital; sometimes staff have to go out and rescue their patients. The group has not firebombed clinics, as its US counterparts have, but staff fear that will be the next step.

The same group targeted a tiny cancer charity, forcing it to turn down £3,000 from the producers of Jerry Springer: the opera. It also, in effect, encouraged its supporters to issue death threats to BBC executives for airing the show. And it was some adherents to another religion, Sikhs, who used stones to persuade the Birmingham Rep to take off a play of which they disapproved.

The respectable faces of all these religions tell us that the thugs are not really connected to them at all. The truth is that church leaders are at least as ambivalent about their armed wings as Gerry Adams and Martin McGuinness are about the IRA.

When Sikh thugs forced the Birmingham Rep into submission, they were defended by the Most Reverend Vincent Nichols, Roman Catholic Archbishop of Birmingham, who said the play was offensive to people of all faiths. Nichols made it quite clear that if the play had been set in a Catholic church rather than a Sikh temple, he would have demanded the right to censor it. He did not say that he or his flock would enforce their view by throwing stones, but neither did he condemn the violence, in which more than 800 people had to be evacuated - mostly families and children, there to see the Christmas show; violence in which security guards were attacked, thousands of pounds' worth of damage was caused, a foyer door was destroyed, windows were broken and equipment smashed.

He did, however, say something very alarming. He said: "The right to freedom of expression has corresponding duties to the common good." No, Your Grace, it does not, for who is to judge what is the common good? In the days when the Catholic Church was allowed to judge it, people were tortured for asserting that the world was round.

Yet Nichols is in the mainstream of current religious thinking on this matter. Every time church leaders want to ban something, you can watch a bishop on television, crumpling his face in dignified episcopal agony and saying, as one did the other day: "Our community is hurting about this." I, too, find it painful when people mock my most cherished beliefs. But I do not claim the right to stone them until they stop doing it.

This is the growing coalition between faiths which Odone identified in November. In the 21st century, religion is regaining the power, influence and intolerance that it lost in the 20th. Over the past hundred years, religion, in Europe at any rate, was partly displaced by the great secular religions: communism and fascism. Throughout its life, Britain's Communist Party attracted many ex-Catholics because it offered a total answer, which they were used to. And in the immediate postwar years, many former fascists gravitated towards the Catholic Church, which (though not itself fascist) offered the authority structure they were used to.

These secular religions behaved just as the old religions had done. They examined the sacred texts - the works of Marx - in the spirit that medieval scholars had once examined the Bible; and they persecuted those who arrived at different conclusions about what they meant in practice. As Catholics and Protestants had once persecuted each other, so Stalinists and Trotskyists did the same.

Today religion is back with a vengeance - and vengeance is often the right word. Amnesty International lists as many as 45 examples of religious persecution worldwide: attacks on Hindus in Bangladesh, a crackdown on the Falun Gong movement in China, Christians held in metal cages and Jehovah's Witnesses tortured in Eritrea, for example.

In Britain, in the name of tolerance, we are paving the way for religious intolerance. We have the most devout Prime Minister since William Gladstone, who is now in effect a Catholic, and a Secretary of State for Education who is a member of Opus Dei, the shock troops of the Catholic Church. This is the first chance religious zealots have had in a hundred years to return us to the Dark Ages, to heretics' courts and witch-burning, starting by criminalising views with which they disagree. To do this, they have to work together - hence Most Reverend Nichols's temporary alliance with Sikhs in Britain.

Catholic, Protestant, Sikh and Muslim leaders embrace each other, for now at least, to demand more faith schools, which the government rushes to provide, and which provide seedbeds for religious intolerance.

Keith Porteous Wood, executive director of the National Secular Society, puts it this way: "The idea of single-faith schools is to inculcate into pupils that the religion they are being indoctrinated with is the truth, and by default others are untrue. The current policy of encouraging the opening of more and more religious schools will come back to haunt us in future generations."

We are treating religious beliefs as a special case, not open to the same rules as any other sort of belief; and we are tolerating behaviour from religious groups that would rightly be stamped upon if it came from anyone else.

Our children will live to regret this policy.