Because it makes sense to do so.
What you call "fairy tales" is a huge part of people's belief systems, in some cases coming before notions of nationhood. In the past, governments trying to shape the religiosity of people have done on so in many ways that are incompatible with freedom in general and caused great harm.
Speaking as an atheist/agnostic myself, the last thing I'd want my government to get involved with is regulating religion. With the caveat that religion should not, in most cases, be an excuse for ignoring the laws everyone else has to follow (the kind of exceptions I think about are things like peyote consumption for shamanic rituals).
If there are problems with things like dress codes or circumcision then those can be covered by general purpose laws (female genital mutilation is outlawed in many places). Dress codes can be rejected by an individual leaving the religious community (something which should definitely be protected by law). Things like not providing adequate health care for one's children for religious reasons can also be punished by law (there have been a number of cases in Canada).
For the rest, live and let live.
Note that this supposedly inalienable right you speak of is not automatically always present: witness the chador controversies in Quebec and France.
So the most compatible approach for a liberal democracy is to remain very hands off, leave religion, and its rejection, as an individual's choice and resist any attempt at state-level preferences with regards to religion.