He meant being something like Chairman of the Joint Chiefs.
There's nothing in the constitution that prevents the President from choosing to take over many of the responsibilities of the Chairman of the Joint Chiefs. The sentiment behind the statement is pretty clear, but the substantive denial of freedom can get lost in uniforms and job titles. What if Musharraf takes off the uniform but still uses his connections to exercise de facto control of the military? That's basically what happened in China in 1989-1997, for example.
President Washington directly commanded troops during the Whiskey Rebellion.