The text of "Charlie on the MTA" was written in 1949 by Jacqueline Steiner and Bess Lomax Hawes. The melody was composed by Henry Clay Work as "The Ship That Never Returned". It was also used for "The Wreck of Old #97". He also wrote "Grandfather's Clock".
In the 1940s, the Boston Metropolitan Transit Authority fare-schedule was very complicated. The booklet that explained it was nine pages long. Fare increases were implemented by means of an "exit fare". Rather than modify the entrance turnstiles for the new rate, the MTA just collected the extra money when leaving the train.
One of the key points of the platform of Walter A. O'Brien, a Progressive Party candidate for mayor of Boston, was to fight fare increases and make the fare schedule more uniform. This song was one of seven songs written for O'Brien's campaign, each one emphasizing a key point of his platform. Will Holt recorded the story of Charlie as a pop song for Coral Records. After many complaints were received from Boston inhabitants who considered Walter A. O'Brien (a Progressive) to be a Communist, they pulled the record. In 1959, The Kingston Trio released a recording of the song. They changed the candidate's name to George O'Brien to avoid controversy. Besides that, by 1959 nobody outside of Boston (or inside, for that matter) remembered Walter A. O'Brien. Walter A. O'Brien finished dead last in the five-person race. He received only 1.23% of the 296,990 votes cast. He later moved to Maine where he worked as a librarian and later ran a bookstore.
The Kingston Trio's performance became iconic. Several groups like The Chad Mitchell Trio, Dropkick Murphys and They Might Be Giants wrote parodies, some even referencing "poor old Charlie".
You can see from the three-chord structure why it became so popular with us budding folkies in the 50's and 60's. You can't get a much easier-to-play hit song. Originally the verse and chorus were sung to the same tune but The Kingston Trio started the chorus higher.