I remember some of the Lost casting sheets had character descriptions, something like "character who leads a hostile takeover of a corporation" which was obviously not entirely accurate, so being called a 'CEO' probably doesn't literally mean a CEO.
Maybe he is in a manner of speaking. After all, CEO stands for Chief Executive Officer. An executive officer on a ship is the second in command. Maybe the chief executive officer is the second in command for all of Starfleet.
Eh, probably not.