The bad publicity Mexico has received is highly exaggerated and mostly in mainland Mexico, not Baja. Sure, there are drug runners and banditos in Baja too. But, drug cartels are not interested in some dirt bag on a rusty shovelhead, they have way more important stuff to do. Don't bring a gun. Machetes are legal and are very useful tools.
Frankly, you should be way more afraid to roll through Detroit or Inglewood than you should be in San Felipe or Ensenada. Read the tips for riding your motorcycle in Baja here, sack up and hit the road!