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One important difference is the Fantastic four were well know as scientists before they became super-powered. They went on a mission and the accident was well documented leading to their powers. It's a known force that the public are able to get to grips with. The mutant phenom isn't as simple and neither is spider-man with his secrecy.
People are afraid of the unknown, The fantastic Four, Captain America, Iron Man et al are not unknown entities but well documented and well publicised super heroes, the others are not.
Read the Marvels, it's a great read about how normal people respond to the growing super hero population, very highly recomended and read it myself, only last week
Personally I find it eaiser to justify this than the way in which DC super heroes are imagined and their place in society
Hey Gary
Good points well put