From what I've seen, Negroponte is one of the good guys -- but it's getting harder and harder to tell.
In this linked article, he is criticized by the left for supervising the creation of the El Aguacate air base in Honduras. The air base was used for US training of Nicaraguan Contras back in the '80's.
I think Negroponte is a good guy. And Bush just gave him the most demanding ambassador post on the planet. He'll earn every nickel he's paid, and then some.
John Negroponte is indeed a good guy.
My only suspicion is that he is highly regarded by both sides of the Aisle in Congress. But that has its advantages.