We tried to avoid leaving our luggage in our trunk while traveling through Spain, but sometimes it was inevitable. When that was the case, we did a couple of things:
1) Clean out the interior of the car--no maps, no brochures, no souvenirs or postcards. Why advertise that there MIGHT be luggage?
2) Do all of your trunk arranging BEFORE you stop and park somewhere...and don't open your trunk once you have parked your car. Do it at a gas station on the way or something. Don't toss a purse or other items in just before you walk away from your car.
When we did these things, we felt pretty comfortable leaving our car and luggage for a while. Obviously, you should have your traveler's checks, credit cards, cash, and travel documents tucked into a travel pouch in your clothes when you leave your other stuff. And don't leave things that will melt (chocolate) or overheat.