I'm sure the Hulk has been in at least three team books. But he's also the guy who Reed Richards and Tony Stark conspired to fling into space hopefully never to be seen again. People ARE terrified of the Hulk. At the point where the United States government was looking a bit askance at mutants they were flat out constantly trying to kill the Hulk and they kept on doing that for decades. Killing the Hulk was a major line item in the defense budget. Heck Canada even tried to kill the Hulk. When the Vision is not part of the Avengers to lend him legitimacy he has been treated with great suspicion and prejudice. Aquaman is the knockoff. Namor is the original. And no, he isn't trusted or admired but that's only fair since he regularly turns supervillain. The problem with the mutant menace thing is not that it doesn't inherently make sense. It's that Marvel has 60 years of tangled continuity to saddle them with endless narrative twists, turns and inconsistencies. At this point nothing in the Marvel universe can make sense if looked at closely. After all they've got a bunch of guys in their 20s who have 50 to 60 years of personal history.
Let me paste an answer I gave elsewhere to this kind of question:
Magneto is a moron. He first brought the existence of mutants to the attention of the general population with terrorist acts that he claimed to be carrying out on behalf of a new race. The other major supervillains don’t usually claim to be representing any group. Loki doesn’t claim to be the champion of Asgardians and Doctor Doom doesn’t strike blows on behalf of people with facial blemishes.
Professor Xavier is a moron. There is no good reason why he didn’t seek out teenagers who weren’t mutants for his school/army of child soldiers. Instead he chose to define the mutants as a distinct and separate minority. Mutants who join more heterogenous teams get a much more favourable response. Mutants tend to come in two flavours. The first is those who are phenotypically unusual from birth and often not in pretty ways. The second are the ones that look normal from birth onward but begin to manifest their powers during the hormonal surges of adolescence. Which means when they actually have dangerous powers they tend to first manifest them during times of stress. So…usually by hospitalizing or killing a family member or a kid at school.
Mutants were for a time by far the most common origin. In order to generate significant prejudice, you need a large enough population that you begin to lose sight of them as individual and only regard them as a group. You stop seeing trees and start seeing “forest”
Some idiot called them “Homo Superior”. Can you imagine a better way to put the backs up of us Homo Inferior?
As for the issue of distinguishing people with acquired powers from mutants without special abilities, well it's certainly possible to make a misidentification and that has happened in Marvel comics both ways. But well-known characters tend to have well known origins and in a lot of cases it didn't particularly matter one way or the other. Nobody cared whether Spider-Man's was a mutant because they were too busy hating him for being Spider-Man or loving him for being Spider-Man. And it's not like the Avengers and the Fantastic Four didn't get their share of haters just for being supers. It's just they managed to win some degree of acceptance by both saving the world and being given government and media acknowledgement of that achievement. Even when an Avenger was a mutant, just being an Avenger would legitimize in the eyes of many people who didn't trust either X-Men, or mutants who tried to live like they didn't have powers.
