The courts ruled that he owed trespass damages caused by the cattle and that he had unlawfully grazed cattle on federal land, in addition to the backlog of grazing fees. Since some of the restrictions on his grazing were to protect the dessert tortoise, I suppose you could say that the trespass damages included irreparable or measurable harm to a natural resource. I suspect the governments agents expected trouble based on previous experiences with Bundy and is the same reason they released a couple hundred head of Bundy cattle they had rounded up to pay for damages. Some where in the mess of it there is probably impeding the duties of a law officer. Maybe creating a public nuisance if his deputies are really stopping cars on a public highway. Someone might find public endangerment an as a possibility. I don't think I want to touch the race issue, but you can suspect the answer.
Here's the court ruling on the charges of trespass and unlawful grazing.
http://www.blm.gov/pgdata/etc/medial...%2010-9-13.pdf