I don't think the comments above are actually addressing faith schools in the UK. They are talking about what are traditionally called 'Church schools', which arose when Britain was a single-faith society.
In the early 1990s, around the time that Prince Charles visited a Hindu temple and changed his designation from 'guardian of the faith' to 'guardian of faiths' it became obvious that it was discriminatory to provide state aid in the form of money to schools of one faith alone (Christian, disregarding the various flavours).
To rectify this anomaly Tony Blair introduced the faith school legislation which opened up funding to any faith, based on certain conditions about not rejecting people of other faiths, etc. He could have done what France and other countries have done and made state education completely secular, without stopping churches providing their own schools out of their own pocket if they wanted to.
The first problem with faith schools is how you define faith, and what is the difference between a cult and a religion: is it just the number of followers and the amount of real estate they own? Scientology is officially a religion and has charitable tax status. David Icke and his followers could easily call themselves a religious faith: their central tenet that the earth is run by shape-shifting lizard people is no stranger than Scientology's and, objectively, no weirder than the story of a being with wings flying down from heaven to impregnate a virgin with the son of god. So who do you preclude from opening a faith school without appearing to be arbitrarily discriminatory?
But the main problem is that they are socially divisive - and this has happened in practice, it is not theoretical. Although they are required by law to be open to all faiths, in practice, all the faith schools have become almost totally attended by children of one faith. This leads to social segregation, misunderstandings between communities, and an inability for people of different groups to understand each others beliefs. Not least, you find the phenomena of 'othering', where social groups really believe the members of the other group to be less than human, and therefore useful scape-goats in times of social crisis. This is happening between orthodox Jews and Muslims in London, not to say the middle-east.
It was once fashionable to bemoan Britain's multiculturalism, but in fact, what you have is plural mono-culturalism, with lots of isolated communities that never mix. Faith schools aggravate this problem. You can find a good analysis of it in Amartya Sen's "Identity and Violence".
It's good to understand that Jersey has not become a multi-cultural society in the sense that the rest of Britain has. If you had a 7% Muslim population and 3% Hindus, Sikhs, Jains, Bahai, etc, and their schools were being funded by the States, it would be different to just talking about subsidies for De La Salle and Beaulieu.
What Blair should have done is ended state support for religious schools, and slowly reduced the subsidy for CofE schools over a decade until they were self-supporting or closed. Since they were up to 90% tax-payer funded anyway, it would make no difference that their pupils were now fully in the state sector.
And the other miscomparison is to ignore the fact that we are living through a period of religious fundamentalism - it is not the slightly bland version of Christianity previously on the menu, which as one commenter noted, did not result in the indoctrination of children, whose parents were not devoutly religious in the first place. Creationism anyone?