I am once again delving into the psychology behind scary things instead of talking about scary movies or books.
All along I have posited that "the other" is the thing that scares us. Something different than ourselves triggers a fear response in most of us. Aliens are the perfect encapsulation of other, we have so little in common, we don't even come from the same planet. However, just their presence usually isn't scary enough to make a whole movie or story. We have to imbue these perfectly foreign things with human motivations like conquest or experimentation. If aliens aren't aggressive, they become cuddly companions like ET or Stitch.
Most movies choose to make aliens as close to humans as possible. In the Alien movies, the facehugger impregnates the victim against their will and the victim gives birth to something that is a cross between the original alien DNA and human. That's why the alien in Alien3 behaved like a dog, it came from an infected dog. We still need things to be recognizable to be frightening. We get that claws and teeth are scary (they are scary on lions here on good old Earth) but if aliens were depicted as living colors or sentient light formations, we go from scared to confused.
Lovecraft is one of the few people to make alien encounters truly alien and that only works on the written page. As with any other monster, the alien reflects our own fears back at us but we have the added bonus of their technological superiority if they come to us. If we come to them, the anxiety of exploration and colonization comes up. Aliens are pretty all-purpose from apartheid metaphors in District 9 to pre-intelligent eating machines like The Blob. While ghosts and vampires don't always work, aliens pretty much will.