The Ayleids were extremely evil! Haven't you read any of the backstory concerning all the grizzly, horrifying ways they used to torture the people who were their slaves? They may have made beautiful buildings, but they were all evil to their core, if you accept the backstory. Their rule was as heartless and terrifying as anything Mehrunes Dagon might impose.
Be well - Pax
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Of course, the Elder Scrolls lore is generally recorded in in-game books and dialogs, as opposed to given to players through objective sources. And I doubt much of the backstory we have on Ayleids was written by the Ayleids themselves, or people who would have been in favor of them, so it's entirely possible that the Imperial accounts did paint the Ayleids as worse than they actually were. Certainly, Imperial accounts aren't going to make Ayleids out to be saints, of course they probably weren't saints anyway, and I'm sure the Ayleids did to some pretty horrible things, but I doubt all of them were as completely evil as we might be led to believe.
That being said, since the Ayleids enslaved the humans, I'd say the humans did pretty much the logical thing to do, when people are oppressed or enslaved, it's hard to see it as unreasonable that they would eventually revolt against their masters.
I mean, would you call the dunmer evil for doing the exact same thing?
Yes, in fact, I would, an evil that needs to be wiped out, preferably with blood, lots of it. It's just the Dunmer that keep slaves, though, those who don't might still be annoying and arrogant, but at least they don't have as urgent a need to die as those who keep slaves, the thing with Dunmer though is that not all of them practice slavery, a few are even opposed to it, and those who are not but don't actually practice it only really seem to defend it with saying "it's the law".