The striker was handed a three-game suspension by UEFA on Thursday, which means that he will miss all of England's group games at next year's tournament.
"I expected a three-match ban, I must admit," Ferguson told MUTV. "Sending-offs usually carry that and I didn't think there was going to be any leniency towards England.
"He is going to miss the group games for England, which is a blow for him and England."
Meanwhile, Rooney is expected to feature for United when they take on Liverpool at Anfield today.