Let's not forget that The Factory Farming Industry and ACTUAL Farms are very different things. Small scale or private family farms need not be offended at the spotlight on large scale FACTORY farm conditions because they aren't even comparable. Apples and Oranges. It would be like a Pharmacy owner getting offended when people complain about street drug dealers. Yeah, both sell pills, but the ethics and practices involved are not at all the same. The large scale factory farms are not even farms by the traditional definition, they're more factories. When farming gets to this level of mass quantity, the details, knowing the animals, hand raising them, etc is often (but not always) lost. My father was a farmer, slaughtered and sold meat, etc, and he is repulsed by some of the factory farm conditions he hears about. He isn't offended, because he knows that doesn't portray HIS farming at all. Like I said, two very different practices.
The main problem for the consumer arises when they want to know where their meat comes from. Few large scale factory farms will let the consumer see the facilities while running & processing, or are simply too far away for the consumer to visit. Therefore, many people prefer to buy from small scale farmers, where they know the owners, or where the owners have a local reputation, etc.
I don't think the majority of people who watch these documentaries actually think local small FARMS are this way, I think they are repulsed at what happens when the meat industry becomes too "factory" oriented, with the lack of quality in product and care for livestock that often results from mass production.
If you take the animals out of the factory farm vs. actual farm scenario for a moment, it's easy to compare. Say you buy hand-made gemstone bracelets from a small craftsman. They're quality natural gemstones, on sturdy cording, with quality lobster-claw clasps. And yes, they're more expensive than mass produced jewelry because of this small scale quality. Now lets say the business grows and sells out to a large corporation, who takes over jewelry production for millions of people instead of thousands. Now it isn't a person or two, hand making the bracelets, but instead a factory. The gemstones are too expensive, so they replace the stones with simulated versions. The leather cording is too expensive also, and doesn't feed through the stringing machine as easily, so the leather cording is now switched to cheaper, thinner nylon. And those lobster-claw clasps are now ordered wholesale, they're smaller and less sturdy. But the result is that you can buy these bracelets much cheaper than you could when the owner was still on a small scale level. This is pretty basic, you could use a thousand examples of small scale production versus large scale.
The problem comes when we go back to the fact that the product is ANIMALS, and MEAT. Unlike beaded bracelets, we now have two much more serious concerns: Animal welfare and our health consuming the meat. Suddenly short cuts in production seem iffy, when it comes to us consuming that meat. And the lack of personal attention actually affects animal well-being. People in general like to think of these animals as being personally cared for before slaughter. It's not as simple as the type of beads used in a bracelet when the product changes to animals, and the resulting meat. It becomes much more personal, on an ethical level and a food safety level.
So bottom line, in my opinion: Are there many factory "farms" that have appalling conditions both for the animals and the resulting meat? Yes. Are there factory farms that have ethical standards and clean facilities? Yes. Is it easy to find out which is which? Not really. Is it healthier, give a better peace of mind, and supportive to local business to buy from small scale farms? Yes. As with the bracelets, the resulting cost is usually higher, but some choose to pay more for the peace of mind of buying locally.
In any case, I still maintain that factory farms are really not actual farms at all, so local small scale farmers need not even be offended. If anything, they should be offended at the use of the word "farm" in factory farming.