Peter Baker of the New York Times has a lengthy and balanced assessment of President Obama as commander-in-chief of the armed forces. Most of his sources spoke on the record, including Defense Secretary Gates. Baker did not seem, however, to have spoken to senior military commanders.
Gates makes some surprising comments: that Obama suggested General Petraeus when he resolved to remove General McChrystal; that Gates and the President were surprised when McChrystal asked for additional troops for Afghanistan after receiving and urgently requested 21,000; and that the leak of McChrystal's request was "indiscipline" rather than a deliberate effort to "jam" the president.
I agree that Gates has been an excellent tutor and buffer for Obama with the senior military leadership. And I don't think Obama has made serious missteps in his dealings with the military. But civil-military relations are a fluid relationship, always subject to challenges.