My old boss (who I constantly talk to) has had a few of his cars in different movies. He had his Zaz in some quirky romantic comedy a few years back. They strapped a smoke machine to it because you know, all Russian cars apparently burn oil. He had one of his Eagle wagons (yes he has more than one) in a made for tv movie that was based in the 80's. And just a few weeks ago he had his DAF Daffodil as a background vehicle in Transformers 3.
As far as I know if you sign up with a production company it's in the contract that if they damage your car in any way they will pay for the costs for repair or replacement.