Jay, I'm probably going to end up on the opposite side of Savage here, too. My read on John Negroponte is that he is one of those men who has the ability to get things done. There are a lot of smart, talented people in the world, but the number of them who can really act and achieve goals without excuses is radically lower.
I'm guessing that President Bush got burned on Bernard Kerik and then thought, "The celebrity strategy for this post hasn't worked, I'm going to name a superbly competent person who doesn't care much about image or headlines. Thus, we get Negroponte.