Rooney was surprisingly left on the bench for Tuesday's Champions League defeat by Real Madrid, triggering massive speculation about his future.
Sir Alex Ferguson attempted to play that down on Friday, insisting Rooney would still be at Old Trafford next season.
Even so, it would have been difficult to envisage a future at Old Trafford for Rooney if he had failed to make the United line-up on Sunday.
He was included, though, and in his preferred striking role alongside Javier Hernandez, with Robin van Persie this time left on the bench.
In his robust defence of his treatment of Rooney on Friday, Ferguson also spoke of his fears about the way his striker was being handled, especially when he is away on England duty.
However, the FA has defended its position, insisting Rooney is treated no differently than any other player on England duty.
"Wayne has not undertaken any commercial PAs (personal appearances) for the FA in the past 12 months and has not fulfilled any more media obligations than other senior squad members," said an FA spokesman.
"As with all England players, we look to ensure that media activity whilst on England duty is sensibly managed."
Ferguson was visibly angered by reports of Rooney's imminent exit when he faced the press on Friday and said: "Wayne will be here next year. You have my word on that.
"The issues that you're all going on about are absolute rubbish.
"There is absolutely no issue between Wayne Rooney and I. To suggest we don't talk to each other on the training ground is absolute nonsense."
The Scot was subsequently quoted in the Sunday morning papers saying that a new contract for Rooney would be looked at at the appropriate time, contradicting reports in the aftermath of Tuesday's defeat which suggested the club could allow him to leave at the end of the current campaign.
The former Everton forward is tied to United until the end of the 2014-15 season and Ferguson expects a new deal to be discussed.
Ferguson said: "There's no issue with his contract, when it has to be renegotiated it will be. We don't want players to leave."
Former Arsenal manager George Graham, however, believes Rooney does have a problem with his fitness.
The Scot told BBC Radio Five Live's Sportsweek programme: "I think with the build Rooney has got he is always liable to put on weight.
"He has got to play regularly, he has got to play every week.
"He cannot afford to have any bad injuries when he has been out for a long time. I think he has got a problem with his fitness."
He added: "For his career, for the next four years he is going to be at his peak, he has got to be very disciplined not only on the pitch in his performances but he has got to be disciplined off the pitch.
"This is probably a little problem that I am sure has been foreseen by Sir Alex in the past."
Graham is unsure whether Rooney's long-term future lies at Old Trafford.
"I have got a funny feeling it won't be," said the former Scotland international, who had a spell at United as a player.
"It is a big call and it might not be Sir Alex's decision, it may be the money men's decision in the background.
"Two years is usually the time you start negotiating again with a new contract.
"Yes, I am sure United will offer him a new contract but it may be less money than he is on now."
Ferguson bristled when asked about Rooney before the start of the cup tie.
Questioned about Rooney's response to being left out in midweek, he told ITV1: "Nothing. It's straightforward. I don't see why you want to ask that question."
To a follow-up question asking whether Rooney 'just has to get on with it', Ferguson responded: "Everyone has to get on with it."