Try and have someone accompany you. Perhaps your sources there, or anyone local that you can trust. They may be more than willing to take you around a little, in return for some money, or little gifts.
Even if it's only to bring you to the bus, or go to the next city/village to meet your next informant...
This depends very much on the context, so I don't know if it's possible at all and how, but it may help.
I worked and did research in Sri Lanka. Once during the civil war, and another time right after it officially 'stopped'.
I'd say as well that careful judgement helps, too. Be alert and careful of course. Other than that I can't give any advise, also I'm not familiar myself with Central America, except with the Dominican Republic which was a great and seemingly safe experience to me, even in the mountains/country side.
Cheers
Dennis