It's one thing to raise questions about the truth of religious doctrines or about the moral authority of religious organisations and leaders - something I approve of and encourage. It's another to seek that religious doctrines or practices be suppressed by the coercive power of the state - something that I totally oppose. People should be entitled, in law, to believe whatever seems true to them, without being regarded and treated as criminals. They should also be entitled to act on their beliefs, so long as they don't breach well-justified and fair laws of general application. We obviously need to have laws against murder, so nobody gets to plead her religion to justify human sacrifices to her god. But if what she does is lawful outside the context of her religion, it should be equally lawful inside that context.
As always, there are some grey areas, but we should always look at issues of substance, not mere formality. Take the recent decision in Switzerland to ban the building of minarets. I suppose one extreme justification of this law might be that it applies equally to Muslims and others - it's not discriminatory against Muslims because no one, Muslim or not, is henceforth allowed to build a minaret. But that would be a silly argument. The law specifically forbids an activity associated with one religion: Islam. It unfairly burdens just one religion, and it can't be justified on secular grounds. If the problem is buildings above a certain height, then all buildings above that height should be forbidden. If the problem is with certain loud noises, then all loud noises should be forbidden at whatever times of day are appropriate. Singling out minarets is a clear attack on Islam as such, and hence a breach of the doctrines of separation of church (and mosque, etc.) and state and of freedom of religion.
I see that even the Council of Ex-Muslims of Britain has condemned Switzerland's actions. This organisation is fiercely secular, and strongly opposes political forms of Islam. Some of its policies do stray into uncomfortable territory where freedom-of-religion issues arise (e.g. its policy of banning faith-based schools). But it is absolutely correct to state the following: The Enlightenment didn't ban church towers in order to successfully push Christianity into the private sphere. The same must be done with political Islam.
Quite so. Political Islam must be opposed, but that does not justify using the law to harm and stigmatise Muslims, many of whom are doubtless as disenchanted with political Islam as any atheist or freethinker. Again:
Believing in Islam or any religion for that matter is not a crime. Neither is it a crime to have minarets in mosques. What are crimes, however, are groups or individuals using religion to threaten people to death, intimidate them, violate their rights, and discriminate against them. Society has to address these crimes and prosecute those who threaten or terrorise people - not ban minarets!