I think you should not be able to be run over in passive mode, however i'm happy with passive mode being disabled in vehicles.
There's too much you can do in a vehicle that could make a passive mode vehicle the biggest griefing tool ever. Also if you want to get out of a situation, once you're in your vehicle, you have about a 90% chance of getting out of there very quickly, unless you're being harassed by a tank.
But being run over whilst in passive mode is a bit silly. It forces people to jump on to ledges and you're in this stupid stale mate until either you change sessions or the griefer loses patience and leaves the area.
Edit: Also what would be the rules to a passive mode vehicle when you are in passive mode but a passenger isn't? In missions it's not possible to blow up your team mates' vehicles when they are in them. So if they applied this in free roam, what would happen when you have a mixture of passive / non-passive mode people in the car. It makes this combination a massive griefing tool.