Christians also have to pay taxes to fund a secular school system where their children will be taught things they disagree with. Not to mention funding abortion clinics etc (wasn't there a thread quite a while ago about a guy who tried to dodge taxes on those grounds?). But we live in a society, sometimes we have to contribute to things we would rather not.
I might not be up to date, and I know the OP isn't about the USA, but didn't Lemon v Kurtzman establish the principle that the government should be able to fund religious organisations if they serve a primarily secular purpose? Such as is most likely the case with these mosques in France, to help integrate the Muslim community into the society and not leave them in ghettos with no infrastructure or anything.
Bookmarks