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Think of it this way, remember Tommy Lee Jones' character Marshall Sam Gerard from The Fugitive? How he could organize a manhunt so well, anticipate what people were going to do? That's his Ranger Favored Enemy bonus at work there. He doesn't hate the people he's chasing (doesn't mean he likes them either), but he does know their tendencies very well.
If there are a lot of human NPCs, well, then I advise those evil NPCs to be subtle in their work and not rouse the ire of the famously vicious Ranger. I.E., don't just send NPCs charging at him directly; have them be subtle. Have them hire a squad of halfling assassins or something he will be less effective against.
This will only unbalance the world if your world is static. If your world is dynamic and changes to suit the situation, then there won't be a problem. When the human evil NPCs see that no human can match the ranger in battle, they won't send humans to get rid of him.