Throughout the world we have shades of gray not black and white. Throughout most RPGs we have this as well. Even games about Good vs. Evil like D&D have room for the Neutral characters and various kinds of good and evil that are out there. Why then, when it comes to NPCs, do so many of us default tot he fact that an NPC that is against the PC must dislike them just for that.
Even better is that by bringing in NPCs that act against the PCs, but like them, you also open the door to the PCs liking people that they may have to act against. The tension you can get when a PC wants to take a course of action, but also doesn't want to bring themselves against a particular NPC.
On the other hand you can also end up with awesome and dynamic relationships where real professional courtesy can shine through. An NPC who doesn't kill the hired guards while breaking in to threaten the PC because he respects him. The NPC who takes the time to warn of an attack before doing something. Things that make your villains stand out from just another Chaotic Evil psychopath with a magical artifact.
Your PCs will notice it and respond in kind. By adding this layer of depth to the NPCs you encourage the Players to add it to their own characters. Once that starts to happen...well, the game takes a life of its own and that's just awesome.
So how do you do it? It's simple. Find something in your PCs to respect, either as a group or in a particular individual, and develop the NPC that would respect that and in turn has a characteristic the PCs can respect. Combat prowess and codes of honor are easy ones to start with. But you can always find something, even if it just means making the NPC as big a scumbag as the PCs are.
Have fun with it. Let them know who the new guy (or gal) is. Let them get to know each other. See what happens when you do.