"Canuck" is a slang word for someone from Canada. It's not usually considered offensive — sometimes it's even affectionate (and Canadians use it themselves in quite a few contexts). It's a regional nickname, like "Yankee" and other terms.
It is likely that "The Rock" simply took the (offensive) word "motherfuckers", and replaced "fuck" with the rhyming "Canuck" (replaced "f" with "can"), to make the word "mothercanuckers".
Thus "mothercanuckers" is a label combining "motherfuckers" and "Canuck" (or, to use Wikipedia's favourite word, it's a portmanteau of the two). It combines an offensive word and a slang nickname.
The humour (if any) comes (I guess) from this combination (of the offensive with the innocuous) — of having used an ordinary nickname to suggest overtones of offensiveness without actually using an offensive word, thus fulfilling the duties of trash-talking presumably expected of the character.