The story that makes the most sense to me dates back to the turn of the twentieth century.  The year was 1914 and US Secretary of the Navy Josephus Daniels, who was appointed to role by President Woodrow Wilson, banned all US Navy ships from serving alcoholic beverages. Needless to say, not a very popular decision with the rank and file, but one consistent with Daniels' views (he would later be a supporter of prohibition).  Since Josephus Daniels was the one responsible for banning alcohol and "forced" everyone to make the switch to coffee, the sailors began calling their cups of coffee a  "Cup of Joe,"But, there is an issue with this theory - namely that there is no attestation of the phrase "cup of joe" until 1931 when it first appeared in a military officer's manual.  Moreover, the explanation for the phrase in that manual had nothing to do with Daniels, but rather was thought to be a shortening of "cup of jamoke", from java + mocha!Another theory put forward by Mark Pendergrast in his book Uncommon Grounds: The History of Coffee and How it Transformed Our World also dates back to World War I and it goes like this: US soldiers in World War I (1914-1918) referred to a serving of instant coffee made by the G. Washington Coffee Refining Company (founded in 1910) as a "cup of George", and that the common abbreviation of the name "George" ("Geo.") was then read as "Joe".

The simplest alternative to all of these theories is that coffee is the drink of the "common man" - or in the US the drink of "average joes".  But where did the term "Average Joe" come from ...?!