Might help to not carry a bag that screams "I'm a camera bag!" and not leave the gear actually showing. When I have to leave my camera in the car and I don't have the bag, I usually pop a limited or XS lens on it, the body fits in the compartment between seats, most lenses fit in the console compartment, flash usually fits in with one or the other. I don't really like to toss it in the trunk because it makes it obvious you're storing valuables. I've had my car broken into before and the thief accessed the trunk through the back seat. Of course now I drive a sonata hybrid and the trunk access through the back seat is a hole barely big enough to stuff your arm through... just enough that if you have to carry something like a long board or fishing rod or something it could fit through... but I think most cars now have trunk access via the back seat.
My wife gets cold on long road trips, so I keep a small blanket in the car (it's actually an electric blanket powered by the cigarette lighter - crazy). Sometimes I'll toss that over my camera bag if I have it in the car. But my bag is just a
nondescript leather bag - it's dark brown so if it's stuck down on the floor and out of the sunlight, it's not obvious, and it's square-ish, so it doesn't look like a purse.
If you were really, really paranoid, you could remove your spare tire and hide your camera gear in the place that goes. Since my hybrid didn't come with a spare tire in the first place, I've occasionally used that area to store things (for some reason it's got a thick styrofoam liner so it's not a terrible place to stash things you want to keep cold, even if there's no lid).
If you have a vehicle where you can remove some of the seats, you could use a bicycle lock or something to clamp your camera bag to the loop on the floor that the seat locks into?