Why are there so many rebellions against the UNSC?

In the games and most of the periphery media, the UNSC is depicted as more-or-less benevolent (besides Halsey, which I'll get to). They protect human colonies and research stuff and... that's about it. However, reading through the Halo wikis and playing the games, you are immediately confronted by just tons of rebellions. There are some early in the UNSC's history, the Spartans are made to fight rebels, Reach starts looking for rebels, Halo 5 depicts a colony that is openly hostile to UNSC, etc. If the UNSC are so good, why are these rebels so ubiquitous? I have never read any of the Halo books about them, so I honestly don't know.

It just makes me somewhat uncomfortable with the setting, and playing as a protagonist like Noble 6, who is explicitly described as a massive killer of rebels. I especially hate how Halo 5 deals with Halsey and her relationship to Master Chief. At least in Reach, Jorge is depicted as respectful but subdued to Halsey, as if he is uncomfortable being around her. Halsey in 5 basically acts like Master Chief is her special little kid, even though she is a kidnapper and child abuser responsible for the deaths of innumerable children. I thought that game was going somewhere when it describes Master Chief and other spartans as emotionally distant and physiologically fucked up by her, but then the game takes a 180 and basically sides with her by making her interrogator seem mean and unreasonable. You know, siding with the monster who killed kids to further a program designed to destroy rebels.

I don't know, there's just something about Halo that makes the setting seem morally questionable but then it never really expands on that in the core material. I absolutely love the setting, don't get me wrong, but I wish it would do a little more to expand on these morally questionable things. Maybe it does in the books, I haven't read them so I couldn't know.