You could also keep your cats indoors(which is safer for them btw). They live longer and then you don't have to resort to physical punishment.
I have three cats and one of them likes to go outside with the dog. He has his own little lead and he loves it. Other than that my cats don't get let outside.
As far as the original post.. I am of the belief oh well they are little paw prints. I suppose if it really bothered me then I would buy one of those tarps that you can cover your vehicle with.
Susan

Moth balls, cayenne pepper, vinegar, citrus... all scents cats find repulsive.

I've also heard dry, recycled coffee grounds work. Leave them sprinkled around the car daily.