My experience with farmers markets here in the central valley of California (where most of the fruits and vegetables are grown in the USA) is that at least half of what is offered comes straight out of commercial boxes. The produce is the 2nd quality (what can't be sold to chain stores) and they get better than chain store price. That said, it is very small volume.
I work for a rather large produce company. That said, I just wanted to point out that while we may sell 12 million boxes of fruit, the company started out as (and is still owned by) a family of farmers. They just kept reinvesting into buying more land and planting more acreage. It is nearly impossible to make a living off of small amounts of land so from the 30's onward, those who were successful slowly got bigger. Those that stayed small typically went out of business. I know that it is easy to see big farms as scary big business, but honestly, most are cooperatives of farmers who simply want to make a living. They aren't out to get people or poison them. They just are trying to provide the grocery stores what they are asking for: consistent condition, high quality produce.
I haven't watched Food Inc (yet) but as far as chemical applications to vegetables (ok I'm not versed at all in veggies, but I am in some fruits), what is applied is what would happen naturally but instead is done at the time the farmer can control it to ensure a good quality/condition arrival to the stores. For instance, ethylene gas is naturally emitted by many fruits (think peaches, nectarines, apples and pears) as they ripen. That is what makes those fruits get sweeter if you leave it on the counter a few days (or ripen in a paper bag if you are familiar with that trick). That is the same gas that is put on fruit to ripen it (think bananas). There would be no way to get bananas to market if you picked them ripe (think how fast they go from green to brown when you get them home.) Instead, they are picked green, shipped, and then ripened in a special room that has the gas in it to bring it to the right ripeness for eating.
I normally don't respond to posts of this nature because honestly it seems to spark a lot of controversy, largely over distrust of big companies... and there is no way to prove a negative (that big companies aren't out to harm people.) But think it through... why would a company want to harm it's consumer? It just doesn't make sense. If anything, a company wants to please its customer, and if it does, it gets bigger because of it. The company I work for is 4 generations of farming families. They started as dirt poor immigrants in the early 1900s. It took a lot of hard work and dedication and love (trust me, I've never met a farmer that didn't love his "babies" - his produce). I've never seen people more passionate about their business than farmers, whether organic farmers or conventional farmers.