Earlier on, when more people had religious beliefs, most intolerant people of course were religious. Now, not so much.

A fair number of people think that a belief in God makes them a better person. That may be, but there are a lot of great people who don't believe in any higher power or afterlife, and I don't see a correlation either way. My suspicion is that most good people who believe in God would still be good people if they didn't believe in God or an afterlife. There are others (on the atheistic side) who argue that belief in God is unreasonable and a sign of a feeble mind, but there's no evidence for that either. I do think certain strains of belief (i.e. fundamentalism) appeal to the worst of humanity, but these don't account for most religious believers.

I think one of the major issues is that the common religious labels (Christian, atheist, Buddhist) are so broad as to be effectively meaningless. You can be a smart, liberal, universalist Christian, a spiritual atheist who believes in life after death, an observant Jew who believes in reincarnation, or an intolerant, conservative Buddhist. (For each of those descriptions, I can name at least a few meeting them.) So any claim made about "atheists" or "Christians" or "Muslims" as a group is going to be nearly meaningless. I definitely think there is a lot in religion that has immense transformative power (for good and bad) but the mere matter of whether a person has religious beliefs or not or belongs to a religious organization seems to say very little about that person.