German blogger Thomas Landen contrasts the way in which the German government treats Baptists and Muslims. Baptists who wish to homeschool their children are forbidden to do so (the government is enforcing a Nazi-era law); children have been forcibly separated from their parents, who were considered a bad influence on them.
On the other hand, the government allows Muslims to engage a wide range of overtly political behavior designed either to segregate Muslims from Germans and German society, or to assert the dominance of Islam.
Landen's explanation: the Baptists pose absolutely no threat of violence, which cannot be said of the Muslim minority. The government is simply allowing itself to be intimidated.