From my understanding, there was a line of people behind him pushing to get on the plane (we all know how much pushing goes on there) and he didn't have an extra hand to pull his pants up. He said he would do it when he got to his seat, which according to him, he did. Apparently that wasn't enough and he was arrested.
Now, like you said, I don't know the entire story, as I wasn't there, but this is what I have gathered from reading about it. If I'm wrong, please correct me, but from all I have read he tried to cooperate to the best of his ability, but that wasn't enough for the flight crew on a power trip.