This term was originally used during slavery or by slaves. The salve master would come to the slave "house" and take liberties with the female slaves. Though the term was not usually said to the "masters" face, if it was said that the motherfucker was coming it was known what was meant.
(The term applied to slave masters or anyone that had authority over the slaves. Slave Masters, Their Sons and overseers).
1.A very annoying, obnoxious, mean person. Similar to words such as Fucker, Douchebag, Asshole, Jerk etc.
2. A person who fucks their mother.(Literal meaning)
Bob:That guy called me words and mocked me!
Jack:That guy must be a MotherFucker!
(Note: No offense meant for the usage of names:)