I think Noel Kingsbury is right on target in this SEED article from last month.
Genetic engineering came onto the scene at a time when both the public had largely lost faith in science and the U.S. public funding of crop improvement was essentially replaced with private funding by international monoliths, such as Monsanto*. The consciousness of the public has completely tangled the concept of genetic engineering (which isn't categorically different than other breeding techniques) with fears of the archetypal monopolistic, unethical multinational corporation. I think the opposition to industrial agriculture also comes from the fear of what happens to the little guy/human soul when new technologies and the economic machine eliminates a former way of life.
Let's try not to get our science mixed up with our philosophy.
*In Monsanto's defense, they've authorized free use of any of their patents to non-profits working to ameliorate poverty in Africa. Wouldn't be great if the pharmaceutical companies did the same and stopped prohibiting African countries from manufacturing AIDS generics?