Small conflicts and disagreements are a natural part of living together and getting along, but to the passive aggressive, confrontation is to be avoided at all cost. This means that they take out their angst in subtle, under-the-radar ways which help them to vent frustration and avoid an argument.
Cut them some slack. Passive aggressive people are afraid of conflict because they don't want to get hurt or be "the bad guy." This means that if you live with them, your frustrations probably stem their unwillingness to be honest about what they think and how they feel. This is how they deal with the world, but nobody can do better until they know better, so give them some time.
Be direct. If a passive aggressive person is mad at you, you'll eventually know, even though they won't say it. All of a sudden the dishes will pile up, the cable will mysteriously get cut off, their music will get louder, or your toothbrush will taste a little off. So every time they do something passive aggressive, call them out on it. Say, "Hey, I noticed that the dishes are piling up. Did you want me to do them or is something wrong?"
Give them every opportunity to express their feelings. Calling them out on the passive aggressive behaviors sends a message that they can't avoid talking to you, and that you really want to know how they think. It may take awhile, but they'll eventually open up if you keep at it. Be ready for them to deny most problems, at least at first.
Resist the urge to fight. They won't fight back. They'll clam up, give you the cold shoulder, tell you what you want to hear, or burst into tears and run away. Even if you're really upset, set it aside and discuss what you're upset about calmly, ask them what you'd like them to do differently, and leave it at that. If the interior of your car smells odd or your right shoe goes missing, you'll know that they're still peeved, so again, call them on it.
Avoid reacting to passive aggressive behavior with passive aggressive behavior. This rapidly shuts down communication and creates paranoia and more misunderstanding. Sometimes passive aggressive people really do just forget about the dishes like everyone else, or just had a bad day and want to be left alone. If you start behaving the same way, neither one of you will get the chance to clear the air. This means that petty issue will become major snags faster than you can say "new roommate."
Lead by example. It's hard to live with a passive aggressive person without being a mind reader, but it can be accomplished as long as you respond calmly and directly to any friction or problems as they happen and then let them go. Eventually, your exemplary behavior will rub off on your housemate and conflicts will decrease as mutual trust increases between you.