Just returned from Puerto Vallarta (we flew) lovely town/city and we felt perfectly safe driving and touring. The border cities are really scary, but the tour will drive through with an escort as quickly as possible. We've done it before without a problem. As for non-refundable, you might look into TravelGuard or similar trip insurance which will provide vacation insurance for non-refundable expenses and travel medical coverage. We took the Tracks Copper Canyon tour when you could get on the flatcars. An experience of a lifetime, had a great time, not a single problem.
