Ferguson revealed that he spoke to Rooney on Thursday to assure him that his decision to leave him out of the team to face Real Madrid in the Champions League should not be seen as a sign he will be sold in the summer.
But he also used the meeting to tell Rooney that his loyalty to the FA is misplaced.
Ferguson feels that Wembley chiefs are too quick to use United's No.10 as the poster boy of English football without giving him any protection in return.
"It's because Wayne is a stellar England player that he attracts so much attention," said Fergie.
"He's the Gascoigne, the Bobby Charlton of his generation. He is the best English player there is.
"I spoke to Wayne on Thursday and I told him he will have to probably go through a bit of s**t this week. That's the name of the game.
"I keep telling Wayne that he's too trusting. I told him, 'I don't know why you do all this stuff for the FA.' He does things for the FA every time he goes down there and they have never helped him once.
"Every time he does anything, they punish him more than anyone else in the game.
"He should be realising that. He shouldn't have to do anything for the FA, but they force him to do it."