This post at Fast Company talks about how cotton subsidies meant to help small farmers ends up subsidising large agri-businesses. One commenter says
It is always the case that programs designed to help the little guy end up helping some large corporate body.
A separate story in the Washington Post called "Dairy Industry Crushed Innovator Who Bested Price-Control System" (also picked up by both Marginal Revolution and Greg Mankiw) talks about dairy programs in the US and provides a case study. One company was operating outside a pooling and price-setting system, and was able to sell milk which was cheaper than other suppliers by twenty cents. It was forced by law to stop!