Rooney reacted angrily to a challenge made by the Manchester City captain on United winger Nani, and he was seen making his feelings known to referee Chris Foy prior to the dismissal being made.
"I have no complaints about Wayne, I don't think it was unacceptable what he did. I think it was a natural reaction to a bad challenge from an opponent," Ferguson told reporters.
"But I can understand where Roberto's coming from because that's what happens with players today, they all appeal for penalties or players to be sent off – it's an unfortunate part of our game."
Kompany and City have appealed Foy's decision.