it is generally-speaking the areas within 20 miles of the US/Mexico border that have the greatest danger. I've never been there, so others may know better, but from what I have researched Ensenada is far enough away from Tijuana for it not to be a problem.
As for driving in Mexico: stick to the toll roads if they're available, don't drive at night (potholes, wandering livestock etc), use a non-descript looking vehicle.
Guerrero Negro is reported to be very safe, very laid-back and great for whale and bird watching. about 4 years ago