I use a Smoky Quartz in the center console of my car for protection of the vehicle. I might periodically cleanse the car with smoke and/or holy water, followed by visualization. I also do a protective shield around my car sometimes and ask for archangels Michael or Metatron to protect my journeys, while envisioning their energies coming down and surrounding my car. If archangels aren’t your thing, there are dozens of deities that protect traveling.
I also used to draw sacred protective symbols (like the equal armed cross, Reiki symbols and the pentagram) over the doors with my hand whenever I left the vehicle to protect it. That is pretty much all I do. You could shield your car the same way you’d shield a room (which was discussed in this post) or you could create a talisman, bindrune or other spell which you keep in the vehicle. Since energy can dissipate over time, it might be a good idea to add focus and energy to whatever spell or method you use periodically. Malachite is another wonderful stone that protects during travels (but it is toxic if ingested).