There are various organizations that have formed to regulate professional sports. When a single such organization becomes very dominant, it is often identified by the sport it controls. Thus, the word "baseball" in the United States might refer to a game played by amateurs, school teams, and professionals, or it might refer specifically to the professional teams subject to the authority of Major League Baseball (the official name of an organization). Within MLB there is an official whose title is the "Commissioner of Baseball."
Since it is basically a private organization, his authority and duties are whatever the team owners in the two big leagues want them to be.
There is an organization of professional football teams--teams that play American football with an elongated ball--called the National Football League, or NFL. Roger Goodell holds the position of "Commissioner of the National Football League," often "NFL commissioner" or "commissioner of the NFL." I don't think he is commonly called the "Commissioner of Football," though.
In any case, "Commissioner of Football" means "the highest official in an organization that regulates professional football."