Speculation concerning Rooney's future at the club was rife last week after he was left out of the United starting lineup for their Champions League defeat to Real Madrid.
When informed that Bayern Munich were the latest team thought to be interested in the striker, Charlton told reporters: "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."
Rooney scored United's second goal during Sunday's 2-2 draw with Chelsea in the FA Cup quarter-finals.