A commander is the person in charge, particularly in the military. If you're in the Navy, your commander gives directions that you're expected to follow.
A commander does exactly what it sounds like: she issues instructions or commands and assumes they'll be obeyed. Although there are other kinds of commanders, you're most likely to find the word describing a military official. The President of the United States is considered the "Commander-in-Chief" of the US Armed Forces. The word comes from the Old French comander, "to order."