St John's supposedly murdered a cox in a boat race once- they had a spike sticking out their boat or something that's why they're called Lady Margaret Boat Club rather than St John's...don't know how true this is though. Not even sure that is connected.
I think by now it's just tradition as St John's has lovely people there but years ago maybe it was seen as being pretentious or something?
I heard one of the Trinities started it because St. John's is richer/nearly as rich. But yeah, i'm pretty sure it's because of the stereotype of a St. John's student. I know Christ's people say it because John's got our land though, if it helps :P
I heard that it has a pretty bad reputation. That's all I know.