I really doubt that a Catholic like Hitler wanted to kill all Catholics.
I don't think Hitler did consider himself a Catholic.
As he stayed member of the Church his entire life, yes he were Catholic (like much of the rest of the Nazi elite), something not even the Catholic Church try to deny.
You seem to have a little bit of an anti-organized-religion chip on your shoulder, as most people who try to claim that Hitler or most of his followers were Christians at all usually do. They were very outspoken against organized religion and professed atheism. That's a historical fact...
