There's a strong undercurrent of fear of strangers and the strange in atomic-age horror. If the object of horror is man-made, it's often caused by a reclusive scientist, mistrusted by the locals (see Fiend Without a Face, for example.) If the horror is linked to an alien invader, there's often a suspicious newcomer (Teenagers from Outer Space, The Human Duplicators, I Married a Monster from Outer Space, or more benevolently The Day the Earth Stood Still and This Island Earth.) Sometimes, it's friends and family acting like strangers that is the give-away (It Came from Outer Space, Invaders from Mars, Invasion of the Body Snatchers.)
A number of people have commented about the Cold War link to this fear. People were afraid of Commie infiltration, and alien invasion is partial code for this fear. However, most people seem to have missed the strong emphasis on conformity that's also woven throughout the Fifties. People were terrified of being different or associating with people who were different. This is in part due to theories of psychology popular at the time, particularly as promoted by Anna Freud (see the documentary The Century of the Self, especially episode 2, "The Engineering of Consent"; for period examples, see educational films about being well-adjusted in The Prelinger Archive.)
You can see these fears out in the open in the Michael Landon film I Was a Teenage Werewolf. The main character is shamed into feeling different because of his hot temper, so he agrees to an experimental technique. You can guess the result from the title. You can see a more light-hearted toying with these fears in '60s TV shows like My Favorite Martian, I Dream of Jeanie, and Bewitched. All of these represent the fear from the viewpoint of the person who's different; xenophobia in atomic-age horror represents the fear from the viewpoint of those who conform.