Sounds like his only real crime was not having permission to use the area he took off or landed from. Surely there must have been a local small airport in the area he could have used. I'm betting this one goes away real fast since it was no big deal. Planes, helicopters, ultra lights, and paragliders fly over all kinds of place and usually if there is some question the authorities just make contact to check it out. Air space for ultralight aircraft are pretty liberal. eCFR ? Code of Federal Regulations
I think the pictures were the real reason he was arrested, but they used trespassing laws to accomplish it.
In my real estate pre-licensure courses, we teach specifically what you own when you buy property. Not only do you own the surface of the land, but a wedge from the plane of the surface to the center of the earth and expanding out to the edge of the atmosphere. Yes, the government has established certain blanket easements for higher altitude flight, but I'm guessing this guy was well below that easement. This is why you can trim your neighbor's trees where they hang over your property, and why utility companies need an easement to run lines underground or overhead through your property. Most people don't even realize they are there, but you can find them at the courthouse. I'm guessing this guy was quite a ways below the established air traffic easements.
As an aside, I don't know that this was necessarily the feedlot trying to hide anything. Cattle can be spooky. A family friend had cattle near town. We have a considerable hot-air balloon community here. Some of them would drop low over his place and buzz the cattle (violating airspace easements in the process). He had nothing to hide, but was fairly pi$$ed when they spooked the cattle and sent them charging through the fences. Now he had to round up his cattle, repair fences, and could be held responsible for any damage they caused to other property. No, I wouldn't want someone flying that low over my livelihood either.
The way I read this article is not so much about law breaking, trespassing or even "food source security/agri-terrorism". There's a serious problem with America's highly industrialized food supply and the industry is always sensitive when it comes to people trying to dig up information to highlight the problems. Of course nothing of this sort in mentioned in the article and I am not familiar with Garden City, so I am just making a wild guess.