Doherty wrote the letter after "ESPN: The Magazine" published a column revealing that Doherty told his players that Duke "still has the ugliest cheerleaders in the ACC."
The comment was made in a team huddle late in the second half of the hotly contested game.
But UNC sports officials and Duke student leaders both say the comment has not caused an uproar.
"I said it as a joke to lighten the obvious tension my players were feeling during the game against Duke," Doherty wrote in the letter. "However, I apologize for the insensitive reference and hope you did not take it seriously or personally."
Steve Kirschner, UNC director of athletic communications, said the comment became public after a team member told a friend what Doherty had said.
Kirschner said the comment made it to the Internet and ended up in the magazine article.
Another possibility is that Curry Kirkpatrick, the ESPN writer who quoted Doherty, overheard the comment while sitting behind the UNC bench at the Duke game.
"It was for the 12 or so players in the huddle," Kirschner said. "Does (Doherty) think that? No. Does he care? No."
He said Doherty also contacted Duke's cheerleading coach Teresa Ward to discuss the situation. "He talked to the (Duke) coach, and they laughed about it," Kirschner said. "She knows he didn't mean it."
Two Duke cheerleaders refused to comment on the incident Thursday.
And Duke student leaders said the comment had not generated an uproar on campus.
Jordan Bazinsky, Duke student body president, said he has not heard much discussion on campus regarding the cheerleaders.
"It's an unfortunate comment; I'm sure it was just a mistake," Bazinsky said.
Whether Doherty meant the comment or not, Brad Morris, a UNC sophomore philosophy and psychology major, said the comment does not taint his view of Doherty.
"I don't care. He can say what he wants," Morris said. "He's God, isn't he?"
Kirschner said there are no hard feelings between Duke and Doherty. "As far as Duke is concerned it's over, and as far as we're concerned it's over."
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