It means that someone likes you a lot. Like they think you're cool and want to be your friend.
Usually used in the bay area. To show that you really really like someone you say, "I fuck with you too tough" or "I fuck with you hella hard"
@hobopelican: here's the link to my new album/movie/song...fuck with me people!! (read: i'd like to precipitously increase my fan base, please check out whatever it is i may or may not be slinging.