That's because matters of faith (including atheism and agnosticism) are pretty central to the core of our being, as humans. People are willing to die to protect these beliefs. Religious freedoms were widely accorded in the aftermath of the 30 Years War where half the population of Europe was wiped off the Earth. Incidentally, religious rights do protect non-believers too or did you forget that non-belief was also once a heresy punishable by death.  Protection of religion is also protection from religion. It means, the state will not interfere in matters of faith. You seem to oppose this as you want the state to interfere in matters of faith so long as they interfere in ways that support your ideological point of view. What about when the state one day interferes in ways that conflict with your point of view? What then?