I think the point isn't that people of faith do bad things but that people of faith sometimes do bad things in the name of their particular diety. People of no faith do bad things as well in addition to doing many good things, people of faith do bad things in addition to many good things.And what have those without faith accomplished that's so good? Those who claim faith in one god or another have done harms in our history, but don't forget about the wonderful secular humanists like Stalin, Mao, and Fidel Castro. Your philosophy has no edge in a debate on morality or the advancement of man.
The problems come from people doing bad things in the name of their beliefs, whether they be religious or secular. In either case it's undeniable that many people have commited some pretty horrible acts because they thought their preferred invisible friend told them to.