I don’t think Mystique has ever been officially a X-woman and Magneto has always been a bone of contention with the other super-groups when he was included in the X-men.
For the rest… here is my unpopular opinion: I understand the opinion of the humans in MU about the mutants. Of course, I don’t condone the persecutions and the massacres. Clearly it’s a over-the-top reaction and it has been done for the sake of drama.
But I understand their fear and suspicions.
Claremont’s X-men showed their humanity and the desire to be a force of good for everyone. It wasn’t hard to be on their side as a reader. So there was a difficulty to understand outsiders’ point of view but, as the X-men are less and less like the ones made by Claremont, it is easier and easier…