The lack of endorsement of faith or religion is not endorsement of atheism. It's an endorsement of nothing.
Good point. Separation of church and state calls for neutrality, not hostility towards religion, or hostility towards non-religion.
In my opinion, the recent interpretations of "seperation of church and state" (and entity not even in the constitution at all) have been an utter witchhunt against all expressions of religion, and that, in my opinion, is hostility towards religion, not neutrality.