Last month, 8,000 public high school students in Montgomery County, Maryland, went home with fliers informing them that no one is "born gay" and offering therapy if they experienced "unwanted same-sex attraction".

The group behind the flier, Parents and Friends of Ex-Gays and Gays (PFOX), isn't the kind one expects to find represented in student backpacks. Peter Sprigg, a board member of PFOX who doubles as a senior fellow at the Family Research Council, recently told Chris Matthews that he believes "gay behavior" should be "criminalized". PFOX president Greg Quinlan told another talk show host that gays and lesbians practice "sexual cannibalism".

A number of Montgomery County parents, understandably concerned about the unusual flier, filed a letter of complaint with the school district. "Everything in this flier makes it sound like the goal is to be ex-gay," said Ms Yount-Merrell, mother of a high-schooler. "It reiterates a societal view that there's something wrong with you … if you aren't heterosexual. And teenagers have a hard enough time."

In response to student questions, Superintendent Joshua Starr agreed that the flyer was "reprehensible and deplorable". But he then pointed out, correctly, that he had no choice in the matter. A 2006 decision by the fourth circuit court of appeals made it clear that if the district allowed any outside groups to distribute fliers through the school, it could not exclude groups like PFOX.

The situation in Maryland may strike many readers as an anomalous event. One would think that it involves fringe characters, is unlikely to be repeated, and can be easily fixed with a new policy.

But none of that is true. In fact, similar events are taking place with increasing frequency nationwide, and they represent the wave of the future in America's public schools. Indeed, at this very moment, the New York state assembly is deliberating a bill – already passed by the senate – that will allow New York's public schools to double as a taxpayer-subsidized marketing channel for extremist groups of every variety.

How did this happen to our schools?

Appropriately enough, it goes back to a lesson we all used to learn in school – but that many people seem to have forgotten. America's founders understood very well that the freedom of religion and the separation of church and state are two sides of the same coin. Only by keeping government out of the religion business can we ensure that religion may go about its business freely. They also understood that, as a consequence, freedom of religion is different from freedom of speech. Indeed, they guaranteed those two freedoms in two separate and distinct clauses of the first amendment.

Over the past 20 years, legal advocacy groups of the religious right – a collection of entities that now command budgets totaling over $100m per year – have been pushing a new legal theory, one that has taken hold of some parts of the popular imagination and that has even been enshrined in recent judicial rulings. The essence of the theory is that religion isn't religion, after all; it's really just speech from a religious viewpoint. Borrowing from the rhetoric of the civil rights movements, the advocates of the new theory cry "discrimination" in the face of every attempt to treat religion as something different from any other kind of speech.

One implication of this novel theory is firmly embedded in the US supreme court's 2001 6-3 decision in Milford Central School v The Good News Club. Justice Thomas stated in his majority opinion that to exclude a group from school because it is religious in nature is to discriminate against its religious viewpoint, and therefore to violate its free speech rights. No one challenges the exclusion of partisan political groups using the same thinking – we all recognize that partisan political groups are partisan in nature. But because religion alone is a "viewpoint", opines Thomas, it is apparently different.

The other important implication is that the establishment clause of the first amendment – the part that is supposed to keep the government out of the religion business – has been diminished, especially in school-related cases.

Until 2006, the Montgomery school district, like almost all school districts in the nation, had a degree of discretion in the materials it sent home with kids. Few people had previously questioned the school's authority to set aside religious and partisan political material, for example. All of that changed when a group called the Child Evangelism Fellowship came to town. The Child Evangelism Fellowship is the sponsoring organization for Good News Clubs, which offer a program of sectarian indoctrination in over 3,400 public elementary schools nationwide.

Backed by the legal advocacy groups of the religious right, the Child Evangelism Fellowship sued the school district and won the right to have its fliers distributed by the schools. The district's policy on fliers, the majority of the fourth circuit court ruled, was not "viewpoint neutral".

The Child Evangelism Fellowship, in partnership with the religious advocacy groups, has litigated similar cases in numerous states, and is, at this moment, suing a school district in Arizona on the question of fliers. These efforts are all done in the name of "religious freedom", and their advocates proudly announce their determination to fight "discrimination". But, in fact, they undermine religious freedom and promote discrimination.

The fundamental problem with the claim that religion is just another form of speech is that it just isn't true. Religion is special; and notwithstanding the new legal theory, our legal and constitutional system rightfully continues to recognize it as such. Thanks to the free exercise clause, religious groups are allowed to hire and fire people and select their members without regard to the laws that constrain other employers and groups. They receive significant tax benefits.

More to the point, religious groups are permitted to preach the kinds of doctrines – that homosexuality is an abomination, for example – for which non-religious groups would be excluded from schools and other government institutions. The cumulative effect of the court decisions based on the new legal theory is to force schools and other institutions to provide state-subsidized platforms for the dissemination of religious beliefs.

So, which religious groups may be expected to take advantage of this opportunity?

Much can be learned from the experience over the past ten years in New York City, after the courts forced schools to become houses of worship on Sundays. Although the new churches represent a variety of faiths, the vast majority are conservative evangelical Christian; a substantial number of these are part of national church-planting movements that happen to preach that same-sex relationships are an abomination.

The Child Evangelism Fellowship is represented at their national conventions by movement leaders who rail against the "homosexual agenda" and promote creationism. One keynote speaker has condemned interfaith marriage, which he referred to as "interracial marriage". The leaders of the Alliance Defense Fund and the Liberty Counsel – the legal juggernauts that have made the new legal theory possible – have produced books whose titles say it all: The Homosexual Agenda: Exposing the Principal Threat to Religious Freedom Today, and Same-Sex Marriage: Putting Every Household at Risk.

They are perfectly entitled to their religion, of course. They are also, by virtue of recent court decisions, now entitled to promote this religion through America's public schools.

The lesson we may learn from our experiences over the past decade is that the founding fathers were right, all along, in acknowledging that religion is more than simply a form of speech. They knew what some of our law-makers and policy-makers may have failed to grasp: when government gets mixed up in the religion business, no outcome is pretty.