The United boss omitted the England international from his starting lineup as the Red Devils crashed out of the UEFA Champions League with a 2-1 loss to Real Madrid on Tuesday, fueling speculation that a switch away from Old Trafford could be imminent for the 27-year-old.
McClaren believes the media have overplayed the significance of Ferguson's decision to drop Rooney, though, insisting the the Scot's call was motivated by footballing considerations.
"Everyone is looking for controversy and some like to find it in the selection Sir Alex made," the ex-England manager told Sky Sports News. "It is premature and obviously stirred up by the media."
McClaren went on to explain that the United boss constantly evaluates his players and their value to the squad as a whole, and insists he sees Rooney remaining with the Red Devils for the foreseeable future.
"Sir Alex will look every week, every day, every season at each individual player very closely in training and games and say what kind of condition they are in and is he still mentally right for Manchester United," McClaren said. "If not, he will have no hesitation in removing a player.
"But for the moment, I cannot see his [Rooney's] future beyond Manchester United."