Being commander-in-chief is very different from being a kind of dictator of the military complex and is strictly circumscribed by law and custom.

For example, all commissioned officers are approved by the Senate, and the Posse Comitatus Act prevents the President from using the military to enforce domestic policy. Congress also has the sole authority of appropriating money to the military and they can attach whatever strings they want.

There is probably not single individual more powerful than the President, but Congress as a whole is by far the most powerful branch of government. The Presidency doesn't even compare. That said, I think what we've seen over the past several years, and will continue to see, is that dysfunctional Congresses increase the power of the Presidency.