There are two responses to this argument.
Firstly, what is it that makes religious belief so specially protected. Many of us hold beliefs we care deeply about, yet do not get the same protected status in the eyes of the law.
Secondly, even if religious beliefs are special, we often don't allow them to be enforced to the point of harming other people. For example, if a religious community were to say that they wish to self-flagellate, we would be alright with that. However, if they were to ask for permission to flagellate all citizens in service to their beliefs, we would say that is too much harm to be causing. We think that religious rights are enforceable only insofar as they do not harm others.