I asked an atheist friend of mine once if he was a non-believer, then why does he even care what others do or think? He said he he would love to leave everybody's beliefs to themselves but he drew the line when their beliefs encroached into his life and his country's laws.
To sum up his point he said "the church enjoys the separation of church and state, but the state doesn't. Drive both ways on a one way street and eventually you'll run into trouble."
Historically and metaphorically speaking, after science was let out of the church's dungeon it came back with a vengeance. I guess we could infer that after the church has run our government down to wedge issues and talking points, we shouldn't be surprised when that "equal and opposite reaction" occurs.