Lupin gets his own room for five likely reasons: 1. He's the unofficial leader of the gang and likes to have his own private space. 2. He likes letting Fujiko have nice things such as the Hilton hotel room. 3. He snores. 4. As he said in the English dub of Part 2 Episode 62, he's an "easily distracted guy" and has to "have it real quiet at night". 5. He'd be very handsy if he shared with Fujiko and all too eager to have sex with her.
Jigen and Goemon share a room because it's easy for the animators to draw them in one place.