It has recently come to my attention that the answer to
this question is a bit up in the air so I will be reporting
reasonable possibilities that I pick up. Some or all may be
urban legend but until I have a sure way to know I will use
1. The U.S. Navy used to serve alcoholic beverages on board ships. However, when Admiral Josephus "Joe" Daniels became Chief of Naval Operations, he outlawed alcohol onboard ships, except for very special occasions. Coffee then became the beverage of choice, hence the term "Cup of Joe."
2. "Joe" is 19th Cent. American slang for coffee.