The new school year will see the launch of a crop of state-funded "free schools", several of them with a religious dimension. The British Humanist Association has launched a new fundraising campaign to support opposition to the spread of faith schools. In a message to supporters Polly Toynbee, who is apparently still president following the A.C. Grayling debacle earlier this summer, bemoaned the fact that there are already around 7,000 faith schools in England and Wales, including nearly a fifth of secondary schools. She described the advent of the free schools as "a growing threat" to mainstream education in this country.

Faith schools are gaining more control over their curricula, which they now entirely set themselves. Those that cannot currently discriminate in their admissions criteria are often gaining the ability to do so. And teachers at Academies and Free Schools are not required to hold qualified teacher status.

This renaissance of faith schools is a paradox in what continues to be one of the least religously observant countries in the world. Until a few years ago, church schools (as they were then called) were largely peripheral to the education debate. The overwhelming majority were (and are) Anglican and most of the rest Roman Catholic. They were generally primary schools. They were successful and over-subscribed, but were not expanding and attracted little interest from politicians of any party. Their existence was a legacy of history - of the time, before universal state education, when church-run schools usually offered the only education available.

All that has changed. Both the last Labour government (especially under Tony Blair) and the present Coalition have been vocal in their support of faith schools, and have legislated to encourage their spread. Even before the introduction this year of free schools, we have seen new denominational schools being built and even former "bog-standard" comprehensives taken over by church authorities and re-invented as faith academies. In some cases, children who might previously have expected to attend their local school are being turned away because they have not been baptised, or because their parents are unable to convince the religiously appointed (and religiously accountable) teachers and governors that they are sufficiently rigorous in church attendance.

For the quality of a child's education, and their life-chances thereafter, to be dependent on the religiosity of their parents, and for this blatant discrimination to be sanctioned by the state, is alarming. For it to be occurring in an increasingly secular society, where most people are indifferent to religion, is almost incomprehensible. What, exactly, is going on?

Two very different trends underpin the modern expansion in faith-based schooling. One derives from church schools' reputation for promoting discipline and good exam results. David Blunkett once expressed a desire to "bottle" their recipe for success. For middle-class parents who can't afford, or who are ideologically opposed to, private education, such schools present an attractive option. Thus they become ever-more desirable, more over-subscribed and more dominated by middle-class families who have the time and determination to do what is necessary to get their children into them. While the "faith" label has become a brand marker of quality, the appeal of these schools has little or nothing to do with religion as such.

Instead, church schools have come to embody the twin desiderata of education ministers: higher standards and greater parental choice. That in itself might be enough to explain their expansion. But there's another factor at play, too, which is the increasing importance of religion in the politics of identity and multiculturalism. The most obvious manifestation of this has been the demand by non-Christian religious groups to open their own faith schools. To many, this seems only fair: once you accept the principle of religions running schools it looks discriminatory to restrict the right to one or two churches. There are well-established Jewish schools, and in the past decade state-supported Muslim, Hindu and Sikh schools have followed.

These moves have been controversial, with opponents arguing that the new schools encourage the development of a ghettoised society. Education should be about bringing children together, not about segregating and labelling them on the basis of their parents' religion. The existing (and new) schools run by the Church of England have largely escaped this criticism. Yet there have been very few non-Christian faith schools created. There are only eleven state-funded Muslim schools, as opposed to more than four and a half thousand Anglican ones. Moreover, partly because there now exist faith schools for other religions, many church schools have felt entitled to impose stricter religious tests on parents and to make these schools more overtly Christian than they ever used to be.

Most notoriously, this leads some parents to fake religious devotion in order to get their children into a good local school. A friend of mine, an Anglican rector, describes a depressing scene he witnessed when visiting a church where he used to worship before his ordination. At the end of a suspiciously well-attended early morning service, most of the congregation queued up to sign an attendance register. He reported that "a vast extension to the church was built simply to accommodate the influx of parents, barely any of whom turn up once their children are safely in the school."

He doesn't approve, not because he dislikes church involvement in education but because he sees it as an abuse of power by the church, which "simultaneously sits in judgement on parents and families, and encourages hypocrisy among them". It also "degrades the sacraments of Christ's Kingdom by making them entry requirements for something they have nothing to do with."

It is anomalous, certainly, that taxpayers who are not religious - and are not prepared to fake it - should be expected to fund schools that discriminate blatantly on grounds unconnected with education. It makes no more sense than would a school that operated an overt preference for white pupils, or the children of Liberal Democrats, or those whose parents support Manchester United.