I guess this fact was obvious before the article. There had to be people on the ground directing U.S. air strikes. The two obvious choices would be U.S. special operations forces or the CIA, and while it isn't necessarily out of the question that special ops are in Libya the use of CIA operatives allows the President to keep his promise that U.S. troops wouldn't be there.
The question that bothers me is: How did the NYT get its information? The use of CIA personnel in Libya was authorized by a presidential finding authorizing covert action, and covert action by definition is never meant to be traced back to the U.S. I just hope that the NYT got its information through some source other than an American government official.