I think there is no signifcant problem as long as you keep your wits about yourself. Anchoring in an isolated lagoon in one of the dangerous spots is not a good idea maybe - but it is hard to find those isolated spots anywhere. I don't follow the US travel advisories but check the Canadian ones and I have found that they are very conservative in their recommendations - as they should be. I remember their recommendations for Ecuador were concerning before we went there and I have rarely felt safer anywhere than I did there. People were incrediblely friendly and helpful and went out of their may to make sure you knew where you were going. I suspect Mexico might be similar.
In South Africa doing lots of boat stuff. Departure north from Cape Town around December 15th. Arrival in the Caribbean around the beginning of February, after 5300 miles or so.