For years comic book writers have been using the X-Men as a metaphor for a persecuted minority group, but in God Loves, Man Kills the idea gets its most ham-fisted treatment. I don't expect subtlety from a superhero comic, but in this story we get images of Charles Xavier crucified and tormented by demonic versions of his students.
I understand that mutants are persecuted in the Marvel universe, but it has never made any sense to me. The X-men are feared and hated because they were born with super powers, but the Avengers and Fantastic Four are loved by the public and the only difference is that they got their powers from accidents. It would make sense if everyone with powers was feared, but to single out a few based on origin stories is so arbitrary. Weren't the Fantastic Four "mutated" by radiation? Why not fear aliens with powers like the Guardians of the Galaxy or fear robots with powers like the Vision?
I must admit that God Loves, Man Kills is a story that probably would not get printed today. A Christian minister is depicted as a genocidal psychopath who quotes scripture to justify murder. Kitty Pryde at one point drops the "n-word" without euphemism as a response to someone using anti-mutant slurs. Maybe the book has just been so over praised that my expectations were too high.