"Since taking office as a wartime president in 2009, Obama has struggled at times to surround himself with military commanders whom he trusts and feels personally comfortable with."

WaPo reports:

Supporters of [Marine Gen. James E. Cartwright]...  said he ultimately paid a political price for giving independent military advice to Obama that sometimes conflicted with counsel provided by Gates — his civilian boss at the Pentagon — and Mullen....

“He was very aware he was providig [sic] guidance that was not in alignment” with the rest of the Pentagon, said a military officer close to Cartwright who spoke on the condition of anonymity to discuss internal deliberations with the White House. But Cartwright felt compelled to give an independent assessment to the president, even if it risked alienating Gates and Mullen, the military officer said. “He was told [by Obama], ‘No, don’t just give me the old line, Hoss. Give me your opinion.’”