There's a number of reasons, but as I understand the main issue is that John Deere is treating their tractor's firmware like the music industry was treating MP3's. They say farmers may own the tractor itself, and the hardware, but they're only licensing the use of the firmware and don't have the right to modify it. (Which can be necessary when repairing a tractor that has many computerized systems.)

They're essentially creating DRM for tractor software that's so restrictive that installing new parts requires access to secret codes in the firmware in order to turn them on, then accusing farmers of breaking the law if they try to alter or figure out these secret codes in order to keep their tractor working without going to a dealer. (According to my basic understanding, correct me if I'm wrong.)