He is however a zionist and wants mutants to have their own homeland separate from baseline humans.

Magneto is more akin to Nelson Mandela than Ben Gurion, at least with respect to Genosha. He came in as a kind of terrorist-liberator and, after a revolutionary insurrection overthrew the apartheid regime, established it as a BRICS style unaligned state.

But then, because Western Writing, he launched a Hitler-esque plan for world conquest that got the mutant population eradicated as a result. The island has been repeatedly rebooted as this ostensibly safe haven for mutants, but typically becomes a giant death trap where the population is wiped out over and over again.

The moral of Magneto tends to be "Stop being radical, you're just going to get everyone killed". Strangely enough, this never seems to apply to the various secret societies and state agencies running around with the giant killer robots that are primarily responsible for these genocides.

I get the sense that Magneto inherited good-guy status just because using him as a rhetorical and physical punching bag has worn thin after 60 years.

especially if you're going with 90s Magneto

Nearly all my X-Men knowledge comes from the 90's animated series and a few of the comics. He literally tries to wipe out humans and/or make everyone a mutant at least twice. He even acknowledges this in the new X-Men 97 series as he tries to atone for it and live up to Xavier's expectations.