Rooney was surprisingly left on the bench for last week's Champions League defeat by Real Madrid, triggering massive speculation about his future.
And Rooney returned to the starting line-up - with a goal - in the Red Devils' 2-2 FA Cup draw with Chelsea at Old Trafford on Sunday.
Reports have suggested Bayern Munich may be interested in making a move for the 27-year-old this summer, and asked about such talk, Red Devils director and former player Charlton said: "I think that is a bit premature.
"I don't know everything that happens at Manchester United, but I know a little.
"Wayne Rooney maybe has had an injury and has not performed as well as he might have done, but that doesn't mean to say that you get rid of him.
"Sir Alex Ferguson came out and said that he had no intention of letting Wayne Rooney go anywhere. You have to abide by that and I believe it, 100 per cent. He is a great player - why should we get rid of a great 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!"