I think it's more relevant than ever in the world, but comic books have trouble with it. Writers don't get it. And those who do are hamstrung by editorial. Part of my issue with Red is that we all know Jean will fail, regardless of what happens. Yeah, she can beat Cassandra, but there's no solution to Mutant hatred. It doesn't make for a great narrative. I also think Marvel has walked away from the idea of regular people being Mutants. That should be the irrational fear for humans.
All the things you point out are why Mutant hatred works in a modern societal context. The exact same thing defines bigotry in the US. You've got white males with machine guns shooting up schools, but DACA kids are the problem? Corporations and government poison entire communities, but gay marriage will ruin society? Our food supply keeps having issues and people are dying, but a black boy with a cell phone is a danger? Parts of Oklahoma average 2 earthquakes a day thanks to wastewater disposal, but transgender people trying to use a bathroom are the danger?
Bigotry is irrational and people use confirmation bias to validate their hate. Fact is there are racists who listen to Black music artists, watch Black actors and cheer for Black athletes, but when a non-famous Black person enters their community, they're calling the cops for no reason. That's America.
I agree with your second point. Read Avengers for generic superhero stuff.