I think humans are afraid of higher beings than ourselves. Why do you think that for centuries we've prayed to appease various "Gods".
Aliens are another example. Any extra-terrestrial being that makes it to Earth will no doubt have higher intellectual properties than ourselves which is scary. Who knows what sort of machines and weapons they bring (If any weapons at all).
Let's take for example the evolution of humans. Generally and with a few exceptions, physical violence is reduced dramatically the more intelligent a random group of humans are. I myself am quite intelligent and there is very little chance you'll find me fighting anyone ever, even someone I know I could best. Whereas the more violent humans use it as an attempt to resolve a conflict they see no other resolution with. Higher intelligence = higher conflict resolving capabilities.
If anything Aliens, Gods, and Artificial intelligence should fear us. For we are the more primitive group and are relatively prone to relatively spontaneous violent episodes.