Imperial Radch comes to mind. Really, a lot of military-focused genre fiction has shades of this. Black Company, Malazan Book of the Fallen, Old Man's War, and similar tend to have main characters that aren't exactly loved outside of their in-universe group. Someone else mentioned Consider Phlebas from the Culture series, but Use of Weapons is another stand-alone from that series that might be worth reading if you're looking for a main character who is hated for a reason.