Mainstream economics does not assume a priori that markets are preferable to other forms of social organization. In fact, much analysis is devoted to cases where so-called market failures lead to resource allocation that is suboptimal by some standard.
Here's a wikipedia entry containing fascinating discussion of agricultural policy. It turns out there are many motivations for the practice.
This government site gives specifics about farm economics. Among other goals, it identifies a rational social objective of preventing emigration from farm states, which I had not considered.
I'd like to pitch for
this school of economics. Every time someone is diagnosed with cancer, every time a forest is clearcut, the GNP rises.
Public policy around food supply is complex and vital. I can't imagine leaving its public policy in the hands of overly-simplified models of social, economic, and environmental implact.