Of course, but as a society we progress and recognize irrational prejudices. Are you seriously saying I should be tolerant of racists? That's dumb.
I personally think religion is a bit silly in this modern age. But it doesn't bother me that people buy into it. It's mostly harmless. It's when religion makes its way into infringing on rights such as these, that's when I have a problem with it.
And if an atheistic viewpoint makes its way into infringing the rights of religious people what then?