They aren't the good guys. A lot (too much if you ask the community) of the fiction is told from the perspective of the imperium/space Marines, but that doesn't make them the good guys.

They go around saying things like "The rewards of tolerance are treachery and betrayal." They clearly are not meant to be the good guys, even in their own stories.

The problem is media literacy is so poor that far too many people look at quotes like that and think "that's a good point". Even the creators have put out press releases about how all the fascists are missing the point.