Actually yes..to name a couple just in my lifetime..East Germany..the Soviet Union..the heads/governments/councils of these countries were shady and just categorically not good..to put it mildly..and many people all over the world believed they shouldn't exist..and the former no longer exists..unfortunately the latter didn't break up even more and still exists, albeit, in a slightly different way..and on the flipside, Russia now thinks certain countries that did break off shouldn't exist and should be part of the Russian "Republic" again (a republic which includes and condones Chechnya by the way)..and it's not just governments that think these things, it's the people too
Does anyone think North Korea should exist in it's current state?..or any country that is highly oppressive where just trying to leave is considered "escaping" and you can be shot just for trying it? how about any number of countries that criminalize being gay? What about countries that condone "honor killings"?
I'm not saying that Krakoa is comparable in any way to the countries and things I mentioned..but it shouldn't be a mystery why people don't want their favorite "superheroes" to be shady or be complicit in forming a country under shady circumstances without (for the most part) any question. There are supremacy aspects sprinkled throughout these books. I'm not going to go through all the troubling things but it should be easy to see why people might not want their favorite characters involved in something like this.
Also, with so many questionable things, I don't see how anyone can fault people for thinking this could be/should be a cautionary tale...if a cautionary tale is not the intention, they're not really doing a great job conveying it.
As irrational as X-men fandom can be, this hardly seems like an irrational point of view
Defending it (Krakoa) without question is troubling though..that goes for characters and fans