I have always been bothered by this as well, however lots of characters in the Marvel universe are hated even though they're not mutants but instead due to lots of reasons related to their actions or perceptions.
Spiderman is a great example, he is portrayed to be divisive of a character in that much of the populace is OK with him and others despise him for his treatment from Jameson, who doesn't like superheroes in general.
Iron Man, Captain America, and Thor are all respected because they look pretty, same with Ms. Marvel and even She-Hulk. However, when it comes to the Hulk (who is a monster), Hawkeye (who was a former criminal), Black Widow (who is a spy, sometimes for the good guys and sometimes for the bad), and Venom (who is also a monster), these guys are not as respected as their better looking or better reputed counterparts.
The "Mutants are allegory for the outsider" is very true, but it's not the whole of it. There are plenty of mutants who can hide their mutant identity and many who cannot. Nightcrawler was despised by the public because he was a monster whereas Scott Summers was given the Medal of Honor. However, many instances of the X-Men relate to personal relationships. Nightcrawler is an excellent example of this, being a gregarious and friendly individual, he made lots of personal friends with normal humans, such as priests and magicians (ok, so they're not that normal...). The X-Men lesson is based on conquering prejudice with knowledge, empathy, kindness, and that extra effort to make a personal relationship between the normal and abnormal people in our society; not through fighting every bigot or showing off how great you are over others.
X-Men doesn't always fit in Marvel because there is so much out-of-the-norm in that universe, but they work to tell a story. To be honest, it may be one of the most consistent and meaningful stories in mainstream comics today.
Spiderman is a great example, he is portrayed to be divisive of a character in that much of the populace is OK with him and others despise him for his treatment from Jameson, who doesn't like superheroes in general.
Iron Man, Captain America, and Thor are all respected because they look pretty, same with Ms. Marvel and even She-Hulk. However, when it comes to the Hulk (who is a monster), Hawkeye (who was a former criminal), Black Widow (who is a spy, sometimes for the good guys and sometimes for the bad), and Venom (who is also a monster), these guys are not as respected as their better looking or better reputed counterparts.
The "Mutants are allegory for the outsider" is very true, but it's not the whole of it. There are plenty of mutants who can hide their mutant identity and many who cannot. Nightcrawler was despised by the public because he was a monster whereas Scott Summers was given the Medal of Honor. However, many instances of the X-Men relate to personal relationships. Nightcrawler is an excellent example of this, being a gregarious and friendly individual, he made lots of personal friends with normal humans, such as priests and magicians (ok, so they're not that normal...). The X-Men lesson is based on conquering prejudice with knowledge, empathy, kindness, and that extra effort to make a personal relationship between the normal and abnormal people in our society; not through fighting every bigot or showing off how great you are over others.
X-Men doesn't always fit in Marvel because there is so much out-of-the-norm in that universe, but they work to tell a story. To be honest, it may be one of the most consistent and meaningful stories in mainstream comics today.