Why not tell him to stop? Why wait until years later? The problem is that their actions make it clear that they didn't have issues with his conduct. Rather, they decided to cut costs and as a result decided to retroactively reexamine behavior that they had clearly condoned, at least implicitly, years later.

He wasn't acting in bad faith - when they asked him to make changes to his behavior with the pass, he did. Every indication is that if the airline had politely asked him to stop booking flights and canceling them without a good reason, he would have. They were, on the other hand, clearly not acting in good faith. That's the issue.