Krakoa and Zionism is a complicated subject, because X-Men and Zionism is a complicated subject. Chris Claremont, by far the most significant contributor to the X-Men, is very openly and proudly a Zionist, and that influences everything he wrote. I don't want to go too deep into this as anon is asking primarily about Krakoa, but there is a reason Claremont wrote Magneto and Charles meeting for the first time in Israel. Claremont has been very open about being inspired by IDF soldiers for how he wrote women, one of the most praised aspects of his X-Men run; "This goes back to Israel. There is nothing so disconcerting as sitting on a bus and having a young lady walk on with an Uzi flung over her shoulder."
Imp mentioned Genosha, which is the foundation upon which Krakoa is conceptually built on, and Genosha is literally called mutant Israel by Kitty Pryde in the text, so there you go.
There's a lot that can also be said about Genosha and being a metaphor for South Africa, but the point is that this is an intentional part of the framing of Genosha, and consciously or not that bleeds into Krakoa.
So, Krakoa. I do believe that Hickman was, as Imp said, genuinely writing Krakoa as a negative thing. There is something obviously cult-like in the "What is he?" / "MUTANT!" rallying cry post-resurrection in the House of X/Powers of X debut series, and the decision to create a blank slate for eugenicists like Mister Sinister and Apocalypse, or Nazis/genocidal fascists like Gorgon and the Fenris Twins, are things we as an audience aren't really meant to see as positives. When they condemn Sabretooth to life solitary confinement in a face worse than death for breaking a law that didn't even exist when he broke it, we are not meant to be on their side. When Magneto says they are planning on using pharmaceuticals to take over the world and use that financial influence in their favour, I do not thing that was intended as a good thing.
X-Men Vol 5 by Jonathan Hickman, sorry I can't give you the specific issue
Now, I know people point to the following page, where Magneto says the following to a group of ambassadors he met in Israel to disprove that Krakoa is Zionist;
The thing is that this falls flat as an excuse, because that is the same language Zionists and colonisers in general use. Zionists claim the language of defense, claim that Zionism is a landback movement, claim the language of indigeneity to justify their colonialism. Many countries who were victims of colonialism were colonised according to the myth of Terra Nullius, the idea of a land without a people, so it is a land that can be freely colonised without worrying about those pesky natives.
I find Hickman's decision to justify this worldview by giving Krakoa no native population at the time of it's colonialisation disgusting, frankly, and it confirms in my opinion that even if Hickman had been allowed to finish Krakoa the way he wanted, there would still be glaring issues in the way the concept was presented, because ultimately as a white, middle-class, seemingly liberal American man, Hickman just isn't equipped to dissect these topics the way they require. The tropical setting of Krakoa, something that should be a massive theme, given that the majority of the significant and powerful members of Krakoa are white, just doesn't really matter. It seems like Hickman used the aesthetic of the "island paradise" as filtered through an exotifying lens to make it more unsettling that something was wrong, as opposed to the island aesthetic itself being wrong and itself being rooted largely in American colonialisation of Hawai'i.
Krakoa does have something approaching an indigenous population, though, who are the Arakkii, a violent, war-like people who were sent to Hell, or whatever. I'm not going to explain the whole plot of X of Swords and X-Men: Red but what you need to know is that these people decide they don't want their native land anymore, and are happy being deposited in space, because the Krakoan mutants very kindly made the dry, lifeless desert bloom with life and now the people can live there, instead, and we don't have to worry about those guys again outside of X-Men: Red.
All of this really hits the fan though once we get into the Fall of X/the Gerry Duggan portion of Krakoa, which is gleefully Zionist in ways I do not think can really be argued against.
Here is Kitty Pryde, in Israel, who's new country has just been massacred by Evil, Scary Terrorists, who now has to slaughter these Evil Terrorists en masse to save herself but also as revenge for them "Stealing her land", "Pushing her people to the brink of extinction". This is very intentional language and a very intentional setting on Gerry Duggan's part. There isn't really a way to write this and not know what you're doing.
Krakoa is, objectively, an ethnostate. Only people with a specific gene are allowed to emigrate there legally, and the only ways you can get in without a specific gene is via marriage to someone who does.
X-Men + Fantastic Four Vol 2 #2
Despite this though, none of the writers of Krakoa seem to be fully equipped to analyse why ethnostates are bad, specifically, and in the case of Duggan actively justify it by starting another mutant genocide that gives our heroes carte blanche to kill as many terrorists as they want, because they brought it on themselves, they attacked our ethnostate and have to be violently, heroically defeated in any way they can.
In case, after all this, you still doubt that Krakoa is an Israel analogue in a lot of ways, here's Magneto next to an Israel flag just before he rattles off all the mutant ethnostates they've lost.
X-Men: From the Ashes Infinity Comic #13
There's more that can be done to explain this further, like the narrative treatment of Firestar, but I hope I've explained enough to convince someone. This is an issue that is larger than just Krakoa, but the political beliefs of Chris Claremont and how that has never really been dealt with in the X-Men due to the sheer bulk of his work and the enduring factor it has. But hopefully by having more fandom discussions and educating ourselves on what Zionist propaganda looks like and how it functions, we can move in a better direction.
