Okay I think I've come up with a BS answer. Since Spiderman is basically "made," it means that once he was once a mere mortals like us, and is more likely to have the same morals as we do. If someone is born a mutant with superpowers, it's scarier since they could have this superiority complex that they could use (with their superpowers) for evil.
Still doesn't explain why everyone likes Superman and is scared of Batman, though.
