In the real world 'the bad guys' are usually not. It is exceptionally rare for anyone to be universally loathed for their evil ways.
Not really. History has more than its fair share worth of monsters -- if they aren't universally loathed, this represents a failing of the observer, not a lack of evil.
King Leopold II existed. He was directly responsible for a regime that may have killed half of the population of a country, and maimed a sizable portion of the survivors, all for natural resources and all with a self-proclaimed humanitarian face, along with a vast array of serious sins. That he ended up on commemorative coins doesn't make the man less obviously "the bad guy": it says that certain Belgians need to do some serious soul-searching. You could not put him, or a pastiche of him, in a setting without basically having Guy Worse Than Hitler as the stage directions. You have Hitler, Stalin, Pinochet, Pol Pot, Mao, dozens more. Even where you can point to monsters that had good intentions, like Qin Shihuangdi, they are still very clearly villains when they start burning books and crushing scholars under giant rocks. Where they only have a couple of small alcoves full of human skulls instead of the typical mountains, you still have people that might as well stroke a mustache every scene. Pancheco and Bordaberry weren't even terribly bad, as economic and social dictators go for the southern hemisphere (damning with faint praise as that and a thousand+ death toll can be) and still make Palpatine look a nuanced master planner by comparison.
And those are just the obvious, relevant, simple examples. There are countless -- literally countless -- modern-day or historical smaller mass-murderers, and the best thing you could say about them is they're 'just' fulfilling demand for hired guns or drug kingpin, and never quite accumulated the power to kill more. There's no amount of dog petting or tipping of waiters that make up for this stuff.
The problem is that these aren't the only sort of imperialist villains in history, or even the majority of them. And when every Imperialist Villain is King Leopold, you either forget about or trivialize all the ones that were Queen Victoria.
On the other hand, you've got an hour and a half (or three hours) to tell a story... Moral Complexity and well meaning people doing bad things for good reasons? Great, maybe if you've got a few sequels to work with and don't mind loosing half the audience along the way.
Meh. This isn't hard stuff. Change three scenes and you'd make the folk a
lot more complicated.
Princess Mononoke isn't exactly a new story. Whether people want complicated is a different question.