I think the easiest way to summarize people being mad at Endwalker story-wise is 'hopes got into an unsustainable place with Shadowbringers'. Like, remember how much the playerbase spiked during Shadowbringers, not just because of the quality of Shadowbringers itself (which definitely factored) but also because of a few other events outside of FFXIV that happened during that expansion cycle. So for a lot of people, it was just straight-up their first expansion whatsoever, and therefore Endwalker is their first expansion they're seeing at launch. There's also a smaller (but I think much more verbose) crowd who instead seemed to look at Shadowbringer's new direction specifically around the Ascians and got their hopes up for a very specific direction that was never all that plausible, and are now upset that they didn't get what they wanted. Basically, we're seeing people who got a bit too high on Shadowbringers responding poorly to a return to the mean, the revelation that Endwalker wasn't going to be 'Shadowbringers 2'.
To a degree, I empathize with both--Endwalker wasn't the first expansion I was there to see the release of, but it was the first expansion that I was actively following the leadup to, and I'd already had a nasty realization of 'the writers don't agree with what I think is a good idea' back in Stormblood. I think something difficult but inevitable to learn after something that seems to exactly fit your interests is that the game isn't being made exactly for you: the developers have their own plans, methods and ideas. And those are good plans, methods and ideas--none of us would be here if they weren't--but they aren't yours. I had to learn that on realizing that Endwalker wasn't going to bring me the only two things I thought I wanted (Chemist and Gelmorra); others are being faced with it on realizing the story didn't have the same view on the Ascians' history as they did, or that Hydaelyn was not in fact the villain, or that the storytelling has much more high-fantasy, idealistic sensibilities than they thought it did. (That last one is what surprises me the most, because Shadowbringers is so archetypal high fantasy that it's structured like a Zelda game, and I think has the lowest bodycount of any expansion no matter how you tally it.)
If it turns out that, when the veil drops and they see what FFXIV has been the entire time, they don't like it as much as they thought they did? That's fine; I'm sure it's a bit disappointing for them, but it's a revelation that had to happen, and I hope that either they realize they still like the game, or move on to something they like more.