In years past like in the 80's when it actually cost more to produce farming products than they got for price, the government started paying farmers NOT to farm. It left a lot of bad tastes in peoples mouths and rightfully so. Soon that changed, along with the structured subsidies, which are NOTHING like they have in Europe.
The link you cited is taken out of context because it actually is a VERY good thing and fits in well with Permiculture, and that is, there are just some locations monolithic agriculture should just not be. The problem is, in this country laws are very mild on landowners. It is a two edged sword because after all the good ground gets taken up, only the marginal ground is left and in many places it is better that these acres are used for wildlife, forests and wetland plantings. Here is an example; in the State of Maine where I live it is perfectly lawful for me to clear cut a wetland swamp and graze my animals over any acre they can get to. Part of me says that is fine, I am paying taxes and I will use it as I see fit, but part of me also knows its wrong to contaminate wetlands with manure when there are better practices. The link you cited is what this is for, to keep these areas out of production which are allowed to be under existing grandfather laws. Can it it be done...yes, but here is an incentive NOT too. So its actually a good thing.
As for subsidies, that has changed a lot, and I will be the first to say a LOT of farmers have grumbled about it. Long gone are the days where you signed your name on the check and were happy. Now it is based on thresholds. Basically the idea is, in order to ensure we continue to have farmers in the future, prices of commodities must meet a certain threshold...or price. Lets say you are raising corn and they determine the threshold is $3.00/bushel. When you lose control of that corn (sell it) in order to get a subsidy, that price has to be below $3.00 a bushel. Lets say you sell it at $2.50 a bushel, then you would get a subsidy (though it is no longer called that but rather an indemnity payment) for .50 cents a bushel...the difference between the threshold and what was paid. But what happens if you sell at $3.01 a bushel? You get nothing because it is above the threshold. Farmers were miffed at first because they got less money then the year before from the government...but they SHOULD HAVE they were making more money because of robust corn prices!
So that is why I say you are confused, they are using incentives to keep farmers from farming land that should have never been put into production in the first place, and they are not really paying subsidies, but only keeping farmers from going belly up if there is a glut on the market for a particular commodity.
I do get one subsidy however that no one seems to know why, but it has something to do with something my Great Grandfather set up in the 1930's, but even then due to "Sequestering" I must pay a 7% tax on that, along with a 14% tax on off-road fuel that non-farmers have to pay...oh the list goes on.
A lot of the reason we like to buy organic is so that we can have confidence in our food and how it was grown/raised. Certified Organic is a way to have the confidence about a business far to away for you to know anything about. Someone's made it their job to check in on that.
Sometimes buying local can satisfy the same need for us. The milk we buy is not Certified Organic, and I bet it couldn't be without changes to their methods. Still, the store is on the farm. We can see the cows, we can see the scale of the operation, we can see how they work, and there are a lot of things we don't like about the dairy business that we don't see going on there. So we can have some confidence.
Price comes in to play to. If we could do all Organic all the time we'd love to, but sometimes it does demand a higher price (which can be a big difference or a tiny one depending on the product. A lot of our canned goods, for example, are priced nearly the same as their non-organic counterparts.) When our kids first start moving from breast milk to cows milk, we buy the Certified Organic whole milk from the grocery (not local, much pricier.) For the rest of us, it's the local milk. It's not 100% organic, but it's a long shot better than the store brand.
Our bodies can handle a certain amount of things that don't belong... but only so much. It's like the drain on a sink: it can only drain so fast, so if you're putting more in than it can handle you're going to run into trouble. So our food choices are often centered around "doing the best we reasonably can". Sometime local food, even if it's not organic, fits that goal nicely.