You can't have true freedom of religion without a full on secular state, completely without ties to individual religions. Of course a lot of people calling for freedom of religion really just want their own religion in everyone else's face, and anything that prevents that is supposedly an attack on their religious freedoms.

Freedom of religion means that your religion is equal to all other religions. Until you can come up with something that makes it not a religion.

And I still say that when it comes to religious symbols, either we allow them all or we allow none, on the basis of them being religious symbols. Beyond that, if we're banning burqas but not crucifixes it should be for the same reason we're banning ski masks and other articles that cover your face. You wouldn't want either of those in a classroom, for example, if you want to be able to communicate properly. It being a religious symbol should not be a factor. If it is, you're actuallly legitimizing the religion(s) of concern in some way.