Why? Because he is coming into his "mature years."
He also compared Rooney to Sir Bobby Charlton and Paul Gascoigne in terms of his importance to England. Indeed he sees the prospect of him breaking both Charlton's England and United goalscoring records.
Now does that sound like a player who is surplus to requirements?
He's English through and through
Indeed, despite Ferguson's obvious frustration when some players are picked for England (and there are seven this time), he will never stand in the way of Rooney's England ambitions.
Maybe we have come to expect too much from him, especially in terms of England?
Bursting onto the footballing scene like a young fireball, he captured everyone's attention. Whether it was his first goals for Everton and his first Premier League strike at just 16, or a hat-trick on his Champions League debut, he has never been out of the limelight.
That must take its toll, even though Rooney has sometimes brought unwelcome attention on himself.
While you could argue that he would have a quieter social and family life in Italy, France or even Spain, he is very much a "home bird," as is his wife, Coleen.
So even when he threatened to leave a couple of years ago it was unlikely that he would have gone abroad. The greatest likelihood was of him crossing the City of Manchester. Indeed he has been linked with them again.
But as he found out last time, his peace and contentment would be threatened if he did, like when hoodies turned up at his house in 2010.
What he said in that MUTV interview afterwards made plenty of people wonder whether it was all a ruse to negotiate a better contract.
From Sir Alex's point of view it is more of a bonus that Rooney is an England player. Apart from only having to travel abroad for half the games (as opposed to Shinji Kagawa, for example), the England camp and matches give him another chance to get himself fully fit.
It also gives games to the likes of Chris Smalling, Ashley Young and Danny Welbeck who aren't guaranteed a regular start. With two trophies still to play for, sharpness is still important across the squad for the next two months.
The smokescreen of being "dropped"
Nobody at all predicted that Rooney would not start the second leg against Real Madrid. With the English media thriving on controversy in a world where they still have to sell newspapers, this was a godsend.
Even despite Sir Alex's assurances since, there are now several clubs rumoured to be interested in the Evertonian's signature.
The tactical superiority that United showed in that Real Madrid match absolutely vindicated the manager's decision not to start Rooney.
The key was in Ryan Giggs and Welbeck. The former was included to contain Cristiano Ronaldo and the latter because he unsettled Madrid in the first tie and had defensive qualities.
Sir Alex also knows that Rooney comes off the bench or starts a match firing on all cylinders after he has not been played. Los Blancos had played Barcelona twice in the week before, and he could have been lethal against a tired defence.
It was not to be.
But that will also not be a reason for Rooney to leave. He has publicly stated his wish to remain for the rest of his career, even as recently as last autumn.
Nevertheless, it probably suited the manager to put his star player in his place. Nobody is indispensable at United. Look at Jaap Stam, Roy Keane, Ruud van Nistelrooy and David Beckham, for example.
Gradually since that threat to leave in October 2010, the balance of power has shifted firmly into Sir Alex's hands.
At the time it had looked as if Rooney and his agent had got away with "holding a gun to the heads" of Manchester United. Ferguson handled the whole situation masterfully with David Gill's help, but the cost was the biggest contract in United's history.
Now there are different plays going on.
Rooney's fitness is the only issue
George Graham put his "two pennyworth" into the debate last week by suggesting Rooney will always have fitness issues. And even Sir Alex has acknowledged that possibility. He even sent him to Nike to get fit after the contract fiasco in 2010.
Now there's no shortage of people who don't like Rooney, so it would be no wonder if some of them thought he would have turned to "lard" by now. Even now he is sometimes compared to Gascoigne and some of the problems he has had.
He's even been likened to Shrek.
Clearly the lad does have some fitness challenges and they could in part be lifestyle related. But to expect him to suddenly pile on weight and his career go downhill seems far-fetched.
We recently compared him to Duncan Edwards who, in an era of pints of beer and fish and chips, was almost a stone heavier than Rooney at just 21. There was nothing wrong with his fitness; he was just a big, strong lad.
Now it was clear to many that the ex-Evertonian was not fit at the start of this season, despite a six-week summer holiday. He looked off the pace in the preseason matches, and that lethargy seemed to carry into the early season.
Clearly, being injured or otherwise out of training is an issue for Rooney in terms of maintaining his stamina, overall fitness and sharpness. He may have scored on Saturday, but like Robin van Persie, he has not been at his best recently.
And that is why a run-out against San Marino may be to his benefit, both fitness- and goals-wise.
The rest of his career at Manchester United?
Well why not?
What some people don't seem to get about United is that whoever joins the club, whether as a junior or a transfer, has to become multi-talented.
Young and Antonio Valencia aren't just wide players, they can also defend. It is the one challenge remaining for Javier Hernandez, because United's game now is about attacking from the back with a high line and defending from the front.
In this respect Rooney represents almost the dream ticket for Ferguson. And some people forget that Paul Scholes started life as a No.10 before dropping further back into midfield.
Rooney is arguably the best all-rounder at Old Trafford. He can drop deep and defend well one minute while volleying a goal in the next.
That indeed may be part of his downfall recently. He tries to do too much. Against Reading, both he and Van Persie were guilty of playing too deep. That is why Sir Alex needs two top-class midfielders on the pitch all the time.
And there is no reason why Rooney cannot be one of them.
The fact that it hasn't happened yet may be down to two things: a courtesy to Paul Scholes (who has not retired yet), and the need to sign another striker if the move is to happen.
In Sir Alex's interview (mentioned at the start of this article), he strongly alluded to the probable move. If Rooney were to start regularly alongside Michael Carrick, especially when Scholes is fit, people would draw the obvious conclusion.
However, if the "Ginger Prince" retires this summer and rumoured target Robert Lewandowski is signed, you can assume that Rooney's next move will be into the "engine room" at United, not Paris St-Germain.
That would suit all parties. Rooney could be played in midfield every match without worrying about rotation. He would always be available as an emergency striker if needed.
In midfield he would get and remain match-fit. But he would also run up and down the entire length of the pitch far less. Right now he is supposed to be a striker or in "the hole" alongside Van Persie. But if midfield isn't producing the goods then he starts to drift back.
Finally, in central midfield he could prolong his career indefinitely.
Tidying up the loose ends
Sir Alex is not beyond playing a few mind games. The arrival of Van Persie and designation as "No.1 striker" has usurped Rooney's former pre-eminence in that role.
He may have genuinely benched Rooney for tactical reasons against Real Madrid, but the media frenzy that followed may have suited the manager's purpose.
If the lad truly wants to spend the rest of his years at United, now is exactly the time to renegotiate his contract.
Financial Fair Play has arrived, together with a possible wage cap in the Premier League. If neither Mr nor Mrs Rooney want him to leave then a reasonable pay cut seems in order, especially for a future potential United captain.
Nobody really knows, but Giggs and Scholes may well be on less than half of Rooney's wage. No doubt other players like Carrick, Rio Ferdinand, Nemanja Vidic and Patrice Evra will be encouraged to join in the Europe-wide austerity also.
There is also the matter of Rooney's private life. While the media seems to luxuriate in the off-field problems of football stars, genuine sympathy seemed to flow Wayne and Coleen's way over the death of her sister.
It can't have gone unnoticed that Rooney has "got his act together" in the past few years. Particularly since the birth of his son, he seems calmer and more responsible on the pitch.
He clearly cared deeply about Coleen's sister and, despite their other challenges in the past, Mr and Mrs Rooney seem to be in a settled phase of their lives.
Born and brought up in Toxteth, Italy or Spain might have their attractions, but you can hardly pop home to see your Mum. It seems likely that Coleen was a major factor in Wayne staying at Old Trafford last time.
But now Sir Alex has the power. There may be a window this summer to re-sign Rooney for a further five years, which would take him until he was 32, after which the club routinely uses one-year contracts.
If Rooney and Ferguson are true to their word, this could herald the start of a whole new relationship and stability in the club, which could help bridge them through to the ultimate arrival of a new manager.
Despite the rumours that have flown in the last fortnight or so, there is no reason yet to doubt that bright future.
With renewed maturity and commitment, Rooney's best years may be yet to come.