i spent around 3 weeks bike touring in northern mexico when i was 18 (a long time ago now). except for coming down with a fever in the desert and waking up with ants biting most of me, it was a blast and i had no problems at all. ( i'm a guy, by the way). after that, i've never cycled in mexico again, but i spent about 2 1/2 years all told during my early to mid 20's, traveling by bus or hitch hiking. in that time, i had 2 scary encounters. once in michoacan (alone) and once in guerrero (with another guy). fortunately, push did not come to shove.
you sound like you've got plenty of experience traveling alone, so i'd say that as long as you use your common sense, you'd probably be ok. there are places in the u.s. where i would avoid going alone, and in that respect mexico is no different. traveling in mexico can sometimes be a real challenge, but mainly through sudden inconveniences: strains stop, buses are canceled, roads get washed out. that sort of thing. the main danger for a cyclist, as wayne noted, would be the many narrow mountain roads.
