My time in Honduras was maybe eight hours, transit from El Salvador to Nicaragua. My Spanish sucks, but there are frequent road checks with armed soldiers/police in Honduras. At one the soldier asked the driver to tell the gringos they had to pay $1 each to pass. The driver laughs, hands the guy a Coke and we roll.
I spent most of my Central America time in small towns. As Cold Pizza pointed out, gangs are a serious problem in Central America; just ask the locals which areas they feel are unsafe.