The reality is that the border towns suck - but you're not planning to hang around there. There's a real turf war going on with the drug dealers, and I wouldn't put it past them to do kidnapping for profit like they have done in other parts of the country. Don't hang around at the border, you'll be fine.
In the end, though, you should have no problem on your trip - the area isn't heavily populated once you get south of Ensenada (where Coyote Cals is, btw) Hwy 1a, though a toll road, is also fairly heavily patrolled with frequent Army checkpoints (the army is far less corrupt than the Municipales, and the Federales are somewhere in between) Baja California is quite friendly and laid back in general and you'll like the trip...
(I think I have a thread left over here from my motorcycle trip south a couple years back)
one warning - Catavena is the last gasoline stop for over 150 miles - you'll wind up buying gas from a guy with a pickup truck full of gas cans there.
(the restaurant isn't half bad, either)