Often, I see DM's claim that monsters should always target downed PC's because they know that they can easily be healed and brought back into the fight (despite the fact that, if you think about it, most NPC's don't have access to magical healing, mind). Now, extending this line of logic, allowing a weak or weakened group of foes to simply retreat means that you'll probably face them again, and they'll be stronger when you do. Better to deal with the threat sooner than later, right?
Like a lot of things, it turns into "It depends." That's certainly a viable line of thought, but there's at least two others I can think of, and there might be more:
1. Is it a trap? Are the PCs you've beat up lures to get you into an ambush? Do you want to find out the hard way?
2. If the PCs are intruders, letting them (at least some of them) get away can function as an abject lesson to others, which won't happen if no one knows what happened to them.