Any time you are in an encounter, other people can see your car on the world map. It isn't just if your car runs out of gas.
If you are close to civilization like NCR, you are going to get hoards of noobs coming in out of curiosity, if you are lucky.
If you are unlucky, you will be attracting some big gang that will blow the shit out of you.
And then you will also attract players that will come in while you are battling the big gang and steal your car with Lockpick.

Right now, I agree cars needs major improvements.
I can't really think of any good ideas other than putting a sensor bomb on the car that will blow anyone that isn't in your faction up upon touching the car. It will damage the car a lot, but also damage the thief a lot.