Actually, there is a fair deal of persecution for a lot of the others in the Marvel Universe. That persecution is just usually framed differently or it is less constant; although in some cases it is even greater.
The Hulk is more widely persecuted than any of the mutant groups - government tracking him down, misunderstanding citizens being afraid of him, groups that think he is responsible for the devastation created by other gamma powered individuals, and the Illuminati kicking him off the damn planet. Spider man during the saga of the six arms was widely seen as a freak. The Thing originally received poor reactions from the public, though this abated fairly quickly. The Inhumans and Atlanteans had difficulty gaining acceptance as well as they were similarly viewed as having acquired powers through mutation. There are probably more examples I could scrounge up, but these are what come to mind first. The Marvel Universe has a lot of persecution, but with the X-men it is very much framed as the prime threat to a continued existence. I think that framing makes it seem a lot more intense and consistent than it seems for other characters and groups, but I would venture to say it can be found in many places and in some cases it may be found to a greater degree than as seen with the X-men.
The Hulk is more widely persecuted than any of the mutant groups - government tracking him down, misunderstanding citizens being afraid of him, groups that think he is responsible for the devastation created by other gamma powered individuals, and the Illuminati kicking him off the damn planet. Spider man during the saga of the six arms was widely seen as a freak. The Thing originally received poor reactions from the public, though this abated fairly quickly. The Inhumans and Atlanteans had difficulty gaining acceptance as well as they were similarly viewed as having acquired powers through mutation. There are probably more examples I could scrounge up, but these are what come to mind first. The Marvel Universe has a lot of persecution, but with the X-men it is very much framed as the prime threat to a continued existence. I think that framing makes it seem a lot more intense and consistent than it seems for other characters and groups, but I would venture to say it can be found in many places and in some cases it may be found to a greater degree than as seen with the X-men.