Take religion out of schools, hospitals and courts of law. That would be my end goal.

I don't personally have a problem with whatever crazy beliefs people may hold in the privacy of their own brains (or privately owned buildings). People have a right to find comfort and spiritual satisfaction in whatever way they wish. But if those beliefs are carried forward and pedalled through political organisations which influence people's lives outside of their brains (or privately owned churches) then it becomes a problem.

It also becomes a problem when those privately owned buildings are exempt from tax and from all normal obligations any other privately owned building would have.

Atheism itself does not have an agenda and should not be politicised. The agenda is, and has always been, that of secularism. And, needless to say, despite the two things often going hand in hand, you don't have to be an atheist to be a secularist. My most intelligent theist friends are also secularists and agree on the importance of the separation of church and state. And Stalin was an atheist but not a secularist (in fact he promoted state atheism which is just as much of an abomination as any theocracy).