I think what it ultimately boils down to is that Krakoa was a desperation move on the part of its leadership on behalf of mutantkind as a whole. Let's not forget that the previous arc before HOXPOX was mutants being subjected to medical genocide in the form of a vaccine that would prevent the X-gene from ever manifesting in latent mutants, a vaccine intended for national, then global distribution to "end the mutant threat," with almost none of the X-Men's supposed allies in human society and the nonmutant superhero community raising that much of a fuss on mutants' behalf, given the X-Men were presumed dead at the time. After that, I could understand mutantkind, even its more heroic representatives in the X-Men, collectively deciding it was time to try something else, since all those years of attempting to win human hearts and minds had proven so fruitless and even counterproductive to their survival as a people.
Although I'd acknowledge Magneto strutting around declaring mutants "the new gods of humanity" put a bad taste in human leaders' (and real-world fans') mouths, given how many of those leaders were complicit in repeated attempts at genocide against mutants, even if only by their inaction and acquiescence, I didn't have much in the way of sympathy. Hell, I admit not having much in the way of sympathy for the "mutants are too arrogant and overreaching now" argument, because after years or decades of trying so desperately to win humanity's acceptance, respect, and even love and being constantly repaid with violent rejection, disrespect, and hatred, I'll say the mutants are fairly justified in finally taking control of their own collective destiny and no longer holding themselves back to appease those who would see them wiped out, whether by direct action or just standing back and letting it happen. That said, with Captain America/Steve Rogers being brought back through the Krakoan Resurrection Protocols in this latest installment of the A.X.E. saga, I am hoping that does lead to (re)building bridges between mutants and humans (and perhaps even Eternals and Deviants/Changing People, too).