I don't think that old/young men Erik Shoah survivor, Charles, Logan and his brother is the problem. It is the classic X-Men stories demand the great discrimination that mutants suffer from. But in the story as told by Feige the "enhanced" since the emergence of The Hulk and "I am Iron Man" have been almost universally beloved figures thus all you have is a different set of powers and maybe a costume.
You have to go outside of Feige's control to see the beginnings of what mutants face in the comics to the treatment of (nu)Inhumans on the Agents of S.H.I.E.L.D, and hinted at on the Inhumans miniseries. Or of the Dr Whitehall, not Red Skull's wing of Hydra of their collecting the enhanced, Inhumans in that specific case for Hive.