Referee Mark Clattenburg awarded a free-kick to Wigan following the incident, which Wigan boss Roberto Martinez felt "quite clearly" warranted a red card.
Although Clattenburg would have had to have admitted he did not see the incident, many had expected that Rooney would be punished retrospectively, and the Daily Telegraph reports that United "were so resigned to Wayne Rooney being charged ... they had explored possible loopholes to spare the 25 year-old from a ban".
Whelan, whose side were beaten 4-0 at the DW Stadium, said he felt Rooney's escape was unjustifiable.
"I cannot understand how the FA can say there will be no further action," he told the Daily Telegraph. "Manchester United is a great club and Fergie is just simply the best manager, but it is the referees who seem to be afraid of applying the law to United and I don't know why.
"Man United get treated a little bit differently to the rest of the football clubs. I wish they would treat Wigan like that. I wish we could get away with certain things that Man United get away with.
"Mark Clattenburg is usually a very good referee. I could not believe that he [Rooney] was not sent off. Had it been one of our players, he would have walked.
"Rooney was only ten yards from the referee and it was a deliberate elbow. It was the swipe of an elbow right across the head and a clear sending-off offence."
He added in The Sun: "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."
Rio Ferdinand, writing on Twitter, has responded to Whelan's comments, highlighting his own four-match ban after he swung his arm towards Hull's Craig Fagan last year.
Ferdinand said: "The FA 'bottle' it with Man utd is all I keep hearing/reading . . . well you never said they 'bottle' it when I got a 4game ban last season . . ."
Wigan captain Gary Caldwell, meanwhile, has said a retrospective ban for Rooney would have been of no benefit.
"The problem with that is, if he gets banned and misses a game against a team round about you in the league, and United drop points, you can end up being punished twice," he told the Wigan Evening Post.
"If we'd have got the decision at that time in the game, 10 minutes in, then great. That would have helped us a lot, but after the event, nothing's going to affect Wigan, so I'm not really bothered what happens to Wayne Rooney or Manchester United."