He's a wise ass but he's no dummy. He just apologized for and clarified those remarks.
It was a poor choice of words but any pol reputed as a lib/lefty is likely to have fewer allies at West Point than a hard core Rr hawk. Eisenhower was the first I know of to give the concept a prominent mention.
Glenn Beck recently wondered what gave Pres. BHO the right to think he could stand in the way of "the Generals."
The demon Stephen Colbert skewered him with the footage:
http://www.colbertnation.com/the-colbert-report-videos/257716/december-01-2009/u-s--army-chain-of-command