It seems to me that even if you had gods coming down for tea with their worshippers every Tuesday, people would still invent something to irrationally believe in. (Look at all the non-religious stories on Snopes... even setting aside the ones about how Person-or-Company X is a godless crypto-Muslim satanist, plenty of things seems to be believed in despite evidence.)

Also my acceptance for others' quirks is directly proportional to their groups' acceptance of me and my quirks. I don't mind a chapel in a hospital, but I get cross when that comes with the dominant religion being able to place limits on my health care. Fictional religions, unless they are in Really Obvious Parable books, generally don't affect my life any more than fictional characters do.