shoreguy pretty much answered your question. actully the warning is mainly for college kids and yes, it is the border towns.
I don't mean to indicate only college kids need to worry, as the border towns are all pretty bad right now, but the warning has been posted in the past week mainly because spring break is just around the corner.
We just got back home from our cruise on the Pearl yesterday. We were in Cozumel last week and there were no problems. I agree that the majority of the problems are on the border towns. I was really surprised to see Cozumel mentioned in the warning.
It is a shame too since we saw a lot of new stores and businesses in the downtown area that have been developed since our last visit there a few years ago.