Why are people afraid of witches, and not the people who burned them alive?

Fear.

Anything that they don't understand they hate. Because it involves possible change.

If you hate something enough that you don't understand it, you are then afraid of it. Therefore it must be destroyed.

Sorry for coming in on this so late.

The Bible says to kill witches. No exceptions.

Fear of women becoming powerful and independent and destroying the patriarchy.

It's easier in a society to fear the ones who are different. The ones you do not understand. The ones who are familiar can commit abominations, and you will excuse them more easily.