I don't think people fear snakes just because of religion.. but I have heard it used as a jusification for their fears. "Well, I kill them/am afraid of them/avoid them/think they're gross because..."

Children learn to fear things from their parents. It is a learned behavior. There are also people with phobias (which are unreasonable fears).

Example:
I was an arachniphobe for the longest time until I actually made myself hold a tarantula. It was like a switch got flipped in my brain. I'm no longer petrified of spiders due to making myself realize that my fears were irrational. This is not to say that you'll see me out trying to find spiders to play with, haha.

Reptiles are also much harder for humans to 'relate' to. We can empathize with other mammals because they tend to dispaly behaviors that are similar to our own. Reptiles do not.

There is no one single reason, but I will say this: All we can do is continue to educate!