Since you have visited Germany, can you confirm something I read a while back about the automatic deduction of church tithes from paychecks?
IIRC, the article said that if you declared yourself a member of a state-recognized church, your employer automatically deducted your tithe (10% I presume) and sent it to the church. This practice, which I assume also applied to synagoges and mosques, was said to lead to a flourishing religious establishment that is detached from congregations they have little accountability to and, outside major holidays, very poorly attended services.
If this is the case, the high atheism rate might, in part, be an economic reaction to the poor post-unification job environment in eastern Germany: declare yourself an atheist and avoid having tithes deducted from your pay.
I never heard of actual believers leaving the churches because of the tax, but there are a lot of people who are not into religion but never bothered to go to the offices and change their religious affiliation. They normally leave when they have money problems or they read another catholic child abuse story.