That is just a problem with thinking any one event or one writer's story is all that defining of the whole of the Marvel Universe. There were plenty of times since M Day that mutants were 'just fine'. Other than stories revolving around Norman Osborn, Red Skull, Cassandra Nova and the Inhumans, mutants have not been all that hated. They have just had too many crappy stories focusing on moping about becoming extinct because those are the stories the writers decided to tell and they just take so damn long telling them, but if those were so definitive, why would San Francisco build a museum of mutant history? Wolverine was giving open tours of his Jean Grey school. Storm and Wolverine were members of the Avengers. Someone hating mutants is just always going to be brought back in to the stories because it is an easy means of making a threat.