Whatever Fergie says about the referees, they shouldn't take any notice.
I saw what he said about the FA before their verdict over Rooney was given, saying if they punished him it would prove that they treat Man Utd differently to other clubs (and not in a good way). Complete psychological trip from him, he knew full well why everybody was annoyed about the incident but he tries to play it to make the FA the villain of the piece in his favour.
Atkinson in the Chelsea game was a ref who didn't care if he did things that would upset Utd. Their fans aren't used to the refs being more hard on their players and so they feel they were robbed.