It's because the person went out of their way to say that the bad reputation is because of the farmers' feelings, rather than just the fact that wolves kill the livestock. Compare:

> He went to jail for hitting her

> He went to jail because she didn't like that he hit her

This makes it sound like she would or should sometimes like to be hit, rather than being straightforwardly the victim of a crime, or straightforwardly because the person committed a crime

You don't? How about "I think they got a bad reputation because farmers really don’t like it when they kill off their livestock."

so, "bad reputation" is unfortunate, X caused it, but it's unwarranted to read that as "X is unfortunate"? It seems like a reasonable inference.

Yeah. It’s always interesting to see how people fill in the blanks.