Is there really a good answer to that though?
Religious beliefs are often the deepest-held beliefs people have... That is about the only thing that stands out. It makes them unique (allegedly) and worthy of some protection. But it still doesn't really make sense, because I have beliefs just as important to me that aren't religious, but I could be persecuted for practicing them.
Like drugs - I think it is my right to ingest what I want, I feel that principle very deeply, it guides me in many ways throughout life. But unless that belief stems from a doctrine laid down by Native American ancestors a thousand years ago, tough titty.
I personally don't think that religious beliefs should be protected anymore than any other belief. The government shouldn't prohibit you from talking about it or trying to propagate it, but it has zero obligation to not regulate those practices which cause harm.