I'm in your camp. It superficial to judge someone based on their appearance. It's the easiest, safest, and laziest way to identify a threat, however.
There's a real problem in the way our brain is wired, but I'm sure we could learn to compensate for that by reserving judgments until we know what beliefs people hold.
We have to believe in something. It doesn't have to be God, but I know that helped me. In all honesty, I think some atheists like Carl Sagan understood God better than some high-ranking priests, but saw him in a different light----he studied how God made the universe and the laws of physics that He legislated.
Thanks for the great question :)