In all fairness, there is a lot of historical background that is needed here. Here is a map of pre-WWII religions in Germany.
http://en.wikipedia.org/wiki/Religion_in_Germany#History
Then after the war, with the assent of America, I might add, Prussia and much of the East was swallowed up by Poland and Russia. The Germans there were either killed or driven out, mostly West. To a great extent this killed western Protestantism and a big chunk of the Catholic territories as well.
The Russians didn’t miss a beat in destroying every church they could, so a lot of clergy were killed on top of those killed by the Nazis.
Then moving forward to the fall of the wall, afterwards, while there was a push to revitalize the economy of the East, missionaries and clergy should have poured in there, but there was only a trickle of some very dedicated individuals.
Much of that could be attributed to the weakness of the churches in the West, which can be compared to some of the more weak-kneed, liberal and p.c. churches in America.
Even today, a lot of East Germans could possibly be brought back into religion, if someone made a serious effort to proselytize them, with something other than the stale and weak version of the West.
I wonder if this athiesm is a holdover from the time of the occupation of East Germany by Russia. People were afraid to say they were Christians. It’s only twenty years, after all.