There are two meanings:
1) The song lyrics are about someone who likes the passion between two lovers who do not get along very well. The romance is bad (no respect), but the sex is very good (because there is anger). Many people believe that there is more passion between lovers who fight and argue. She says "I don't want to be friends" because if they were friendly, their sex would be less passionate.
"I want your ugly, I want your disease" means I want the ugly and diseased sides of your personality, because your bad sides make everything more passionate.
2) The Music video is about Lady Gaga's Bad Romance with the music industry. She is changed by them and people attempt to buy her. She appears to be ruined by them, but in the end she destroys them.
Hope that helps!