As others have said, a car is not a good place for a handgun.
In my area, vehicle larcenies are generally always the top crime. It is often a crime of convenience/opportunity. There for a while, we had this crew of three juvies that would walk the subdivisions and appartment complexes looking to see who left their car door unlocked. They would steal anything from the cars, pens , key chains, flashlights, sandals, just minor stupid stuff.
Then we had the guys that would just drive through neighborhoods looking into vehicles. If they saw something of interest (aftermarker stereo, radar detector, GPS, PDA, Cell phone) they would either bust out the window glass, or they would wedge the window and knock it off its track. Wedging the window glass was the preferred method as it was quieter.
The next crew we had worked in teams. You had a couple of vehicles that would drop the guys off in the neighborhoods/subdivisions. The vehicles would then circle the area scouting for the police so they could alert the guys on the ground. When the guys on the ground would finish looting , they called someone in the car for a pick up.
We had several other groups/individuals with slightly different tactics.
It got so bad in my area, that my department actually posted a public service announcement, giving the community advice on how to minimize their chances of becoming a victim.
As I have told others....If they want to get what's in your car/house, they will get it. For every security measure, there is countermeasure. Our criminals are getting smarter and smarter.
The bolt on safes are a good idea, but not perfect. These dudes are usually toting equipment to pry with, so the safe(containing the gun) would be pryed off the floor and taken to a better location to be hacked open. Small safes generally scream "STEAL ME" to theives.
Its better than nothing though.
Most of the time when I show up to a vehicle larceny the main focus was the front of the cabin. The console, radio, glove box, etc. Most of the theives in our area are looking for something fast, easy, and portable. Something they can pawn quickly so they can go get their fix. We normally don't see too many ellaborate motives.
I tell people to make their car look boring as possible inside. No bags, backpacks, purses, or wallets. Do not leave your GPS', MP3 players, or radar detectors out in the open. Don't even leave their cords out in the open, that is also a sign that something expensive may be inside. Most of the time the theif will look in your car, and if he doesn't see anything in your ride that's worth his time, he will move on. I have seen this many many times on the surveillance videos at Walmart while investigating a larceny.
Like others have said, the best place for your gun is on your hip, not in your car. If you must leave it in your car, hide it well and make sure you have the serial number written down somewhere .