I think the issue we are considering is more complex than this.
One element at hand is that we are playing a game, and that game effectively give results the players desire, or don't desire, based on choices. But, that game is also set within a fiction, and the game does not, by any means, depict the entirety of that fiction.
GM and players combined, then, have some challenges - how do we remain true to the overall fiction while also playing the game well? The game is built around exciting conflicts, the time at table largely spend resoling those exciting conflicts, and we only have so much time to play. If I only have a few hours every few weeks to play, I have to maximize the value of those sessions.
And, let's face it, NPCs and monsters who are basically nice folks do not intrinsically generate exciting conflicts. So, the GM isn't really incentivized to spend much time on nice folks. That leads to the players not being incentivized to treat figures in game as basically nice folks - to do so is sub-optimal in a game-play sense.
There are some solutions: The players can just bite the bullet and sometimes be at a disadvantage. The GM can include a modicum of stuff that's less exciting, to establish that players shouldn't be sociopaths...
On the game-design side, you can reward the players for some behavior. Many flaw systems are of the from, "You get a bennie if this flaw makes some difficulty for the characters." You can treat PCs like they have a "heroic behavior" flaw, such that they get a bennie if they treat something they see as basically a nice person, and that turns out to be a bad choice.
This last allows the GM to largely hold to keeping with most NPCs and monsters being right bastards, while still having the PCs act like there are good people out there in the fiction that might just happen to be here in-session.