I don't know much about the guy, but when your boss asks for the material, I think his request should be honored...all the moreso when he's the President. Also, he could release some of the more "benign" material to get his critics off his back.
I'm guessing that the President asked Negroponte about the documents and that Negroponte advised the president not to release the documents at this time. I'm also guessing that the President took Negroponte's advice.
There is no evidence whatsoever that John Negroponte is holding these documents against the President's wishes.