Ahh, I didn't realize it was a percentage of income tax. It was explained to me by Germans as tithing, according to the idea of donating 10% of your annual income to the church.
I'm not necessarily for or against it, and it does seem pragmatic for the government to automatically collect it on the church's behalf. The part that does seem strange to me is that you have to renounce your religion to opt out of the automatic deduction, but I understand it's a cultural difference. I'm more used to the idea of contributions as voluntary.
(I'm not German or religious, just an Australian who is a fan of Berlin & Germany and often considers moving there.)
