Well think of it this way
1) They are the "Empire" and have it right in their name and are fighting "Rebels" and "Natives"
I don't really think that every
Empire is automatically evil, and every
Rebel and
Native is automatically good...
The USA would probably count as an Empire today.
2) They have a legion of faceless uniformed soldiers who while they don't have helmets that completely cover their faces, partially do so.
So basically all knights, anyone who wore helmets at any time, fighter pilots, and of course, let's not forget
astronauts.
3) They have superior resources and wealth AKA the Overdogs.
So anyone matching #2 from the USA has three strikes against them now.
4) They are overseen by a large evil organization that watches from the shadows
What large evil organization? What.
5) and right at the start of the game they try to kill you... and the second thing you see them do is kill someone else.
From their point of view, you had just made an illegal border crossing at the exact point where Ulfric Stormcloak and his men were waiting, undoubtedly to meet you...
6) They do not have a legitimate right to rule and are enforcing their laws onto a country that by all means has their own methods of teaching things
You've been listening to Stormcloak propaganda, haven't you? The Empire has been ruling Skyrim for ages. If Ulfric Stormcloak wants to rule instead, he has to prove that he'll be a better ruler. Of course, he can't, because he's a racist megalomaniac, leading a pack of racist thugs, and worst of all, he's in the pocket of the Thalmor, who are using him to weaken Skyrim (and hopefully divide it from the Empire).
7) I THINK they also outlaw cults... but that could be the other side.
Eh?
I honestly believe they wanted the Imperials to be "the bad guys" of Skyrim and just botched their storytelling and made them by far the most likable faction (Mostly by making the other faction kind of... insanely genocidal)
I don't think either the Imperials or Stormcloaks are supposed to be particularly likeable in Skyrim. You're supposed to start out thinking the Stormcloaks are good guys, but if you visit their cities, look around, talk to people, and listen to them, you'll see that they are pretty much racist jerks who want to fight a civil war just because the Imperials were forced to sign away the right to worship Talos in a humiliating treaty. And instead of fighting the Thalmor / Aldmeri Dominion, who imposed the treaty, they fight the Imperials, because (a) they're jerks, or (b) the Thalmor has Ulfric in its pocket (you find proof during the main quest).