starting after WW1 the "General of the Army" or if you prefer Supreme commander has always been more of a political job than real good generalship. Eisenhower was great at mending fences between U.k. French and American relationships but he wasnt really that great tactically. MacArthur was sort of an idiot and yet he somehow was given command of the U.S. forces in Korea until Truman fired him. Patton was marginalized because he wasn't PC, but he was clearly one of the Best U.S. Generals in WW2 but had to play second fiddle to Bradley and Montgomery even though he was often in the right about what the German army was doing or thinking.
And a much more recent example is General David Patreus wanting to arm al-nusrah with weapons to fight isis regardless of the fact that they are an alqaeda front. Meanwhile General Mad Dog Mattis was marginalized because he said something off the record about letting Assad and Russia do in both and he was forced to resign from centcom. I guarantee McChrystal would have still been the commander if he hadn't challenged President Obama despite the fact that he is obviously a pretty mediocre general as well.
There are probably more examples of this going even farther back and what got me thinking about it was the fact That Napoleon got most of the credit his good generals did and I started thinking about U.S. history and its mostly the same thing. Why does it happen?