As far as 40K is concerned I think it mostly comes down to the main faction of the franchise being a hyper religious, fascist nightmare and GW shitting the bed when it comes to presenting any real alternatives. Every faction is at least a little evil or extremely selfish. This leads to the very fucking evil Imperium coming of as “one of many” or “not THAT bad compared to Chaos”.
However, I don’t think this was the result of intentionally propping up fascists as cool and good and more the result of corporate ghouls not getting satire and as a result removing those elements from the narrative until we have arrived at the current point in time. Where we are told by GW that the Imperium is a fascist shitshow and is surviving DESPITE being so shitty. While pretty much all of the novels are portraying the Imperium as surviving BECAUSE they are so shitty. If any of the other factions were definitely good this wouldn’t be an issue.