I have been to Honduras within the last year, traveling to remote areas doing a humanitarian mission. Some required a helo insertion. We were in a large group, and had armed Honduran Army guards, but even then never saw anything that remotely looked like a threat. Big establishments do have armed guards as a sign of stability and respectability, not risk. These could be stores, factories, etc. We also traveled with a contingent of Honduran nationals, so they knew where to go. (tried to scam a ride in a Tucano as well as a night helo mission, but that's another story)
On the other hand, on the commercial flight back, there was a US couple in front of me who had been traveling alone in the back country and decided to go swimming on their own. They were robbed at gunpoint and lost everything. To me, this was more stupidity rather than a reflection of risk.
Overall, like anywhere, a little common sense would go a long way, but in speaking with our people who spent a lot of time in the cities, they never felt threatened or at risk. They always traveled in at least a pair, and always had a cell phone or other comm capability. Again, this is all common sense.
It is a wonderful and beautiful country, lush and green in the mountains. The coffee was outstanding, and I understand the local cigars are good as well. Well worth visiting, and I look forward to returning.