A lot of media in speculative fiction has characters with magical powers, and those characters are often introduced in opposition to characters with no magical powers whatsoever. Think of the X-Men, whose powers are an allegory for discrimination and prejudice in the real world. When a universe has both powered and non-powered people, the story should, at some point, discuss the implications of a world where one side has an inherent ability to do something that the other side will never be able to do. Unfortunately, many stories never venture into the conflict between powered and non-powered people, and the ones that do don’t manage it very well.
Who’s to say that Muggles couldn’t have helped out in the war?
Lady Geek Girl and Friends 