I think the three of them have fundamentally failed to understand each other there tbh.
I don't think AP was declaring religion the root of all evil, just saying that it can be powerful enough to trick otherwise decent people into acting in predjudicial manners. Manners which without the influence of religion, they might think more critically about.
When I was a super-religious Christian fundamentalist, it's not like I went around cackling with glee at the hopes of bringing down some non-believers. For example, when it came to homosexuality, I didn't dislike gay people, but I felt that if Jesus thought it was wrong and bad, then it must have been a really bad choice to make (at the time I thought it was a choice), just as one would smoke or drink. I honestly thought I was doing the right thing by trying to get them to turn away from being gay. I didn't want them to go to hell. My intentions were very good; but my course of action was negative, and wrong. Religion can make a good, decent person do things that hurt others.