Like many other Bob Dylan songs the meaning of this one is somewhat cryptic. Who is Quinn? What are all the people waiting for? What's going to happen when he gets here?
Well, if you are the kind of person who finds such things interesting read on... otherwise get outta here. To me Dylan lyrics are like a cryptic crossword (which I am hopeless at). I don't think it's valid to say that 'this or that is definitely what this song is about,' but is interesting to explore what he might have been getting at.
Theory 1 - based on actual facts: Quinn is an eskimo. In fact, Quinn is Anthony Quinn, an actor. He was in a movie called The Savage Innocents, in which he played an eskimo. In the movie, Inuk (Quinn) must avenge his wife according to eskimo law by killing a priest (of course, how do your laws work?). He is pursued by mounties who capture him but then let him go because they realise they must respect his culture's laws. So, we have an eskimo. We have 'Quinn'. We have religion. It seems quite possible that Bob was just one toke over the line and watched this movie and decided to write a song about it.
Theory 2 - based on rampant speculation: Quinn is Jesus. The people are building ships and boats and generally standing around looking nervous, as seen when God decides to get biblical on their asses. Everybody's in despair, but they are waiting for Jesu-Quinn because he's going to bring redemption.
Theory 3 - based on what some guy on a bulletin board said: The song is about the war. Quinn is America, and everyone is pretty unhappy with the way things are going until he gets there to save the day. This theory has a little merit, but not much actual evidence.
What Bob said: "I don't know what it was about. I guess it was some kind of nursery rhyme." Yeah. Reeeal helpful.
Anyway, it's a good song. You should listen to it.
Incidentally, the correct title of the song is Quinn the Eskimo (the Mighty Quinn). Just so you know.