The subsidies obviously don't specifically say, "big farms get this benefit, fuck the little guy!".
It takes the form of favoring monoculture farms (where economies of scale are more pronounced, but also the environmental impact is largest), or requiring significant compliance expenses and bookkeeping that smaller farms cannot handle (because the cost of bureaucracy is often fixed, so it is relatively higher the smaller the farm), or have been designed to favor farms in specific regions (where the majority of farmable land is already owned by a few large farm corporations).
This is one of the better sourced articles on the subject I could find in a quick googling (interestingly, it comes from a libertarian think tank, which makes them interesting bed fellows with the food justice and local farms movement): http://www.downsizinggovernment.org/agriculture/subsidies
Here's one from another, more left-leaning, source (but with almost no references, just opinion): http://opinionator.blogs.nytimes.com/2011/03/01/dont-end-agr...
The Michael Pollan books (specifically, The Omnivores Dilemma) do actually cover this in some detail, as well, and with good references, though it is a small part of the book.
I'm surprised so many people on HN think it is even a little controversial to suggest that large farms are favored by current regulation, enough that several people are requesting references. I kinda thought it was widely known. So, that's an interesting bit of news for me.