Lots of people ride Baja on their own, but you MUST have some knowledge of the riding areas and good mechanical skills in case you break down. I've ridden there twice on tours and the riding conditions are excellent. This is a very bad place to get lost, hurt or breakdown.
Many who ride on their own stay at St. Veronica's (not sure of spelling) near Tecate. Decent rooms/food and a large parking area. You can use it as a staging area for many long day rides. I don't have contact info, but I'm sure you can find it by doing a web search.
If you ride solo, you may want to purchase a Baja GPS guide. I would never consider trying to ride solo without one. Good luck.
http://www.bajagpsguide.com/