The forward was left out of the starting line-up for United's Champions League defeat to Real Madrid last week, triggering intense speculation about his status at Old Trafford.
Although manager Sir Alex Ferguson rejected talk that he was willing to let Rooney leave United this summer, and subsequently selected the 27-year-old for Sunday's FA Cup tie with Chelsea, rumours are bound to continue for some time.
Yet Charlton, whose records as top scorer for both United and England are under threat from the former Everton man, is not concerned Rooney might be heading for the exit.
"I don't worry about Wayne Rooney," said Charlton.
"There is no way he will ever be allowed to move on, because that is not the way Sir Alex Ferguson works.
"Wayne has been our regular goalscorer - and he scores fantastic goals.
"If he scores a great goal, he'll think 'right, I'll get another one'.
"Not only that, he has an influence on the rest of the team.
"Just because he has some competition, I don't think that is a problem."
Nevertheless, there are enough examples of Ferguson ditching extremely high-profile players not to take the status quo as being certain to be preserved.
And even though the wounds are still raw, it would seem the events of last week are likely to fuel the Scot's desire to have another tilt at the Champions League rather than meekly step aside, as some have suggested could happen.
"I think Sir Alex will be there for the rest of time," said Charlton.
"He is such an enthusiast for the game.
"He is a marvellous manager and whatever happens, he will get the best out of his team.
"What happened against Real will have hurt him a lot but I don't see why we can't win the Champions League again under him, even if it is much more difficult because the opposition is so much tougher."
As ever with United, though, talk of transfers out is accompanied by the potential for a big-name buy arriving.
Gareth Bale has been mentioned, along with Robert Lewandowski.
However, both of those would be eclipsed if Cristiano Ronaldo made a shock return to the club he left for a world record £80million in 2009.
Charlton is loathe to heighten expectations at a return for the 28-year-old, who received such a warm reception last week even though his goals turned the tie Real's way.
But he has no doubt the Portugal superstar left a legacy from his time with the Red Devils that will never be erased.
"Signing Ronaldo has never even been mentioned in any of our board meetings," said Charlton.
"But he did go beyond being just a great player for us.
"He was just the right sort of person Manchester United had been looking for.
"But I once saw Real Madrid trying to get a player from another club, and I didn't think very highly of it.
"I didn't think it was right then and I still don't now.
"Cristiano is a great player, who scores phenomenal goals and he loves the club - but he is not our player."
Charlton was speaking at a press conference in Rio de Janeiro ahead of the Laureus World Sports Awards.
He was flanked by Bayern's honorary president Franz Beckenbauer, who said: "I would be very, very happy if Wayne Rooney decided to come to Bayern Munich, but is this a rumour or is it true? I don't know!"