Wrong MTA.When that song was written Boston's transit system was called the Metropolitan Transit Authority (the MTA).And NYC's transit system was,and still is,referred to as the MTA (but I don't know what it stands for).
Some years later (can't recall when) the name of Boston's system was changed to the Massachusetts Bay Transportation Authority (MBTA).
The song you refer to mentions Scolly Square...Roxbury...and Jamaica Plain,all sections of the City of Boston (Scolly Square became "Government Center" after the song was released).
Uh...like maybe I was joking?
Anyway, as for that mythical doomed rider on the Boston MTA: his wife threw him a sandwich every time the train roared past; why didn’t she put his fare in one of them?
;^)