Agreed - for the longest time, the meta narrative never made sense to me: why are mutants feared and hated more than Avengers, Fantastic Four.
Maybe the Krakoan era has shown mutants are a problem of scale. They combine their powers in ways that can / do terraform planets. As a nation with space exploration ambition, they attract alien conflict. Their unique tribal conflicts also tend to produce reality simulations.
How many times have mutants “snapped” their fingers vs Thanos’ “snap”?
Did the illuminati cause incursions or secretly do a bad job managing an unwinnable situation? IIRC - there would be no heroes reborn alternate universe without Onslaught.
Perhaps it’s not that Avengers and Fantastic Four, etc don’t find themselves wrapped up in similar situations. It’s that mutants tend to spur / cause the situations.
Not unlike Xavier’s original fear.