It depends on which of Honduras' neighbours you're speaking of.
I wouldn't overstate how great things are in Guatemala or El Salvador. I mentioned the human rights problems in Guatemala related to Canadian mining. There are ongoing issues of impunity, where just this morning it was reported in The New York Times that a general convicted of genocide has had that case overturned. In El Salvador five activists fighting Canadian mining companies have been assassinated. Again, there are levels of impunity that go back decades. I wouldn't overstate how much better things are there. Though you're right, in Honduras the situation is much more dire.
I think in part what happened was that you had a stronger social movement emerge in Honduras over those last several years. The moderate—and I don't want to overstate this either—shift by Manuel Zelaya to the political centre-left, by placing a moratorium on mining exploration and development, slightly raising the minimum wage, opting into Petrocaribe, which is associated with Hugo Chavez, was greater in Honduras than in El Salvador or Guatemala. It has played a large part in the kind of reaction that you're seeing.
I don't think it's necessarily that the elite in Guatemala or El Salvador are so much better than their counterparts in Honduras, it's just that in Honduras they've been pushed in a way that they hadn't been since the days of the Cold War.