My experience of riding in Baja as well as the majority of mainland Mexico is you are safe. Avoid flashing money around, especially after dark in drinking establishments or where prostitution is happening (strip bars, clubs) and don't travel after dark (riding conditions and more bad guys out).
Don't brag about your riding exploits/destinations. Don't be a loud and "ugly American" type traveler. Be respectful to locals serving you and don't complain unduly about service, food, etc.
Stay away from resort areas or at least the bar scene.....if you want to get drunk, do it at your hotel/ motel rather than at local bars.....you become such an easy target in those circumstances.
A current ride report re: Copper Canyon points out that some areas have Citizen Patrols that are armed locals keeping a watchful eye for strangers passing through.....you may not notice them, but they sure have noticed you (not Baja so much....more mainland).
Baja outback rancheros keep in touch frequently and actively by cell phone and 2-way radio.....they are your friends....they know you are there. While the kids like stickers, gifts that are useful might be a better idea if you feel the need to "hand out trinkets to the natives".
If you buy gas from an outback location (barrel gas), pay whatever they ask and don't try to "get a deal"....they may not accept payment sometimes, nor a tip (propina)....in which case you DO offer them some money "por los ninos", a gesture they will likely appreciate.
Do NOT expect US dollars to be the currency you use....you are in Mexico....use their money.....you local 7-11 doesn't accept pesos, so realize you are in THEIR country....be respectful.
If you are 4:20 friendly, be VERY careful who you enjoy that with.
Get south of the US/Mex border by 2-300 miles as quickly as possible....more bad guys and desperate folks in the northern part of Mexico.
Learn some Spanish....be respectful....have a great time....ignore the State Dep't....it is an instrument of fear mongering.