The Manchester United forward was caught by television cameras elbowing Wigan Athletic midfielder James McCarthy in the side of the head. At the time of the incident, referee Mark Clattenburg chose to award a Wigan free kick. No punishment was given to Rooney.
The FA have now retrospectively decided that no further punishment is needed for the England forward.
Speaking about the decision to the press, Mr Whelan said: "It sends out a terrible message. Something is wrong when a top international like Rooney is seen doing something like this, as clear as day, and is allowed to get away without being punished.
"If it was any other club or player, you can bet your life he would have been sent off. But officials seem intimidated by the words 'Rooney' and 'United'.
"Manchester United are allowed to get away with things the rest of us get pulled up for. And you can't have one set of rules for one club and another for the rest.
"I don't care what the FA say about the matter being dealt with at the time by us getting a free-kick. They, and everyone else in football, know justice isn't being served here.
"The FA will be delighted they can hide behind their rules and let Rooney off, as they are frightened of taking sanctions against him and his club."
The Latics chairman is likely to be pulled up for his comments by the FA which is quite apt given that the comments are in themselves a defence of why Mr Whelan should not be sanctioned.
Meanwhile it is rumoured that Howard Webb is fuming with Mark Clattenburg after Sir Alex Ferguson kicked the former out of bed last night to make room for this weekend's hero.