There's a difference between having a nuanced, multifaceted villain with sympathetic traits and giving a villain who kicks puppies into trash compactors an unjustified heroic turn just because "everyone can be friends now!"

cough naruto cough

That last sentence is the critical one. People who see their real-life political/ideological opponents as mindless, inhuman strawmen, and then project that strawman onto movie/game/television villains (sometimes accurately, sometimes not) and whine when said villain is not treated like a mindless, inhuman strawman, but an actual human with believable reasons for why they do the bad things they do. Often they just want the catharsis of watching a representation of their opponents get beaten up.

For a recent example, I've been seeing it a lot lately with John Walker from Falcon & Winter Soldier. People getting really steamed over his portrayal because they wanted him to represent white privilege and/or police brutality, and be a mindless raving bigot with no redeeming qualities instead of a flawed human being.