I see that this could work in some games but not all of them. For instance: Kingdom Hearts and their Heartless/Nobodies/Unversed. These three groups of baddies all work for one thing: your death, which is understandable(they wouldn't be baddies if they didn't). However, the nature of them are different from your common bandit/rouge knight, that being that they are single minded in their mission.
Their mission? For the Heartless, it was to seek out and devour hearts, leading to the heart of the world and eating that. They come in swarms from the darkness, and the darkness in peoples hearts, meaning that if someone has so much darkness inside them, they will turn into a Heartless. The problem with this baddy and fear? They don't care if you kill off an entire planet full of them, if there's any darkness inside some one, they will be there. If there are hearts anywhere, they will be there to feed off of them.
The Nobodies I can see having some fear in them, but at the time of KH2, their leader Mansex Xemnas was stronger than them and more powerful than the mobs of white moving bags with zippers that you fought through out the game. They, just like the heartless, are aiming to obtain hearts, but only to be whole again. Since the Nobodies are created when someone loses their heart to a Heartless, they are basically hollow shells wanting to be full of life again. Because of this, their drive to regain their hearts may over-ride their fear of you or their leader.
Now the Unversed, from KH: Birth by Sleep, have no reason to fear you regardless of your planet-killing status. They are essentially made from emotions from the game's big bad's dragon. May I also mention that said dragon is all of the evil incarnate of one of the protagonists. Meaning that they are not only innately evil, they are made from chaotic emotions and only show signs of flat out killing you, or others that got in the way, on the spot. You can argue that since fear is an emotion, and that they are made of emotions, they should also feel some fear, but I could argue that what if the dragon decided not to put any emotion in them that would hamper their people killing behaviors.
I'm gonna end this saying that yes, NPCs in some games should feel some fear and run away when they see your character pop up. However, if the enemies in the game are like the ones that I posted, then they shouldn't feel any fear at all.