I have been down to Baja many times and never really had a problem.
Just hold to the saftey rules for Baja which also hold true for most places in the world.
1. Don't drive at night. Bad things happen at night anywhere in the world. Mostly, there is a lot of unfenced livestock in Baja that like to lay on the warm roads at night. If you hit a cow or a horse, your trip is over and more than likely, you will have to pay for the animal as it is considered your fault.
2. Safety in numbers
3. Don't flash cash or wear lots of cheesy jewelry.
4. I generally abide by the 100 mile rule, I get past the first 100 miles of the peninsula and feel much more comfortable for camping and the like as there are drug and crime problems more concentrated closer to the border.
However, I have spent many safe and peaceful nights in Ensenada and La Bufador.
5. Make sure you do not have any guns or even spent rounds in your vehicle. Any one of those can send you to the can.
6. Be polite to the military and let them search your car at will. Offer them a soda and there will be no issues if you have nothing illegal. (guns, drugs, personal defense knives)
8. Go the speed limit, especially through town. Don't give the local police a reason to pull you over. Plus, the roads pretty much suck down there and have no shoulders, don't be fooled by the toll road between TJ and Ensenada as that is the best it will get. Watching your speed can save your life.
9. Have fun! Happy Thanksgiving.
Jeb