He said that the terrorists had "courage", and that "we" were "cowards" for using cruise missiles.
He later attempted to clarify himself by saying that he was talking about the politicians being cowards because of the way they were using the military in this fashion, not that he thought the military were cowards. This is why on the O'Reilly Factor tonight, O'Reilly brought up the fact that Maher was essentially calling Clinton a coward by saying this, since he was the one who ordered the military to be used in this way, which Maher attempted to duck.
As repugnant as he is with some (most?) of his opinions, I was watching his conversation with D'Souza, and I truly do not believe he was attempting to call the military a bunch of cowards. However, if this is what runs him off the air, I won't complain.
He evidently forgot General Patton's philosophy of war: you don't win wars by dying for your country; you win wars by making sure that the other SOB dies for his country.
That's why we shoot cruise missiles from far, far away at the other guy, so our guy stands a much better chance at not dying for his country.