Yes there were and are some people from the Catholic Church that are evil. You can say the same thing about all of humanity as a whole. And yes it is a human flaw factor that is involved.
I have never nor will I ever say that I am a perfect human being because I am Catholic. To the contrary, I grapple with my demons on a regular basis. The people serving the church are the same. Sometimes we fall.
But to keep holding the church(and that includes worshiper’s like me) accountable for things done in ages past is unfair.
I do not worship Pope Benedict. I do not worship the Bishop’s and the Cardinals, but I do worship Christ as a Catholic. I do not do this because I am ordered to or because I am brainwashed. I can leave at anytime, and choose not to despite the fact that the people running the show at the Vatican are not perfect. They aren’t supposed to be.
Donohue was not addressing all of the church’s dark history. Just the usual lies and garbage spewed about by the haters.
My take on this, which comes from this article alone, is that Penn Jillette was dredging up the church's dark history. So, is that history lies and garbage and if so what dark history would Donohue have to address?