Absolutely.
Not only does human discrimination against mutants make perfect sense, but Magneto is almost certainly right that they are in a war of self preservation and one side needs to exterminate the other.
Also, mutants probably can't coexist even with each other and should be exterminated for the benefit of the planet.
We like to pretend that we live in this amazing world of rules and laws, but the truth is, laws and rules are still enforced by military might. No matter how civilized we have gotten, nothing at all has changed in the most primitive argument, Might Makes Right.
What does society and law mean when you have someone so powerful you can't enforce those rules?
"Oh but there are good guy mutants"....
We have always lived in the Wild West. The faction with the best weapons always holds power.
What happens when someone can just be born with better weapons, bigger guns, and more firepower than anyone else?
Even if you have a group of well meaning X Men, what happens to societal stability in the face of high end reality warpers like Franklin Richards should he just decide to say "fuck being a good boy".
The only answer I can think of is someone like Xavier.
Does anyone not understand the horrifying moral implications of one person being able to mind control everyone on earth simultaneously?
Even if you think he is morally incorruptible, what if someone else is born with that same power but stronger?
How do you build a functioning growing society where every random kid can have planet or at least society ending powers?
How would our society be if every person got issued standard a nuclear briefcase bomb?
Magneto is right in the sense that humans cannot coexist with mutants. But he is short sighted in not realizing MUTANTS cannot coexist with mutants. A society where people are born with such... reality defining (LITERALLY) natural advantages, you can't build a stable society.