It’s an allegory for the civil rights movement with prof. X as MLK Jr and Magneto as Malcolm X. In proper allegorical fashion this means it can be representative for any form of civil resistance by a repressed class, including the fight for gay rights.
This is exactly how I felt. There is always a response that “it’s intentional. Unreliable narrator…blah blah blah.” Which doesn’t make it better. It’s that “jokes on them I was only pretending” meme, but in literary form.