Let's face it, ideologically, the X-Men are basically wishy washy centrists. Why? Because the villains on both sides actually have valid points.
For the mutants, the message has like never change: Discrimination is wrong. What right do people have to harm a someone who's mutant power is like have purple skin or something? This is what makes Magneto right.
On the other hand, how many mutants have gone on rampages either out of malice or just because they couldn't control powers they get when they turn 15? I mean, if she didn't have a moral compass, Storm could fuck over the entire planet. Kitty could phase through to get bank records. And we saw what happened in the opening of X2. This means that William Stryker is right.
So you're at an impasse when very unfine people on both sides spout valid reasoning and the X-Men are stuck trying to play good cop and failing at that. Meanwhile, innocent humans and mutants would get fucked over by the evil mutants and humans.
So yeah, Xavier was wrong.
How can the villains be right and Xavier wrong when Xavier is trying to do both things
Xavier, like Magneto, is showing the world that mutants deserve every right as regular people (live life in peace, gain an education, etc...)
and Xavier, like Stryker who worries about mutants going apeshit, helps mutants deal with the sudden gained power by teaching them how to control their powers mentally and physically so they can help society instead of destroying it.
He does this all in his school.
How is Xavier wrong for having his elite students be the defenders of peace for mutant AND Human kind?