Rooney has been heavily criticised for his recent form, and was even booed by England supporters during the recent international break.
However, despite leaving his captain out of the starting lineup in each of the last three games, Mourinho talked up the respect United have for Rooney ahead of Monday night's showdown with Liverpool at Anfield.
"He was not booed by Man United fans," he told reporters.
"To be honest, the last match when he went to the warm up I was feeling Old Trafford was behind him and immediately supporting him during the warm-up before he came on against Stoke.
"I think at Man United he feels at home, at Man United he feels the respect he deserves. Not at Anfield, obviously, but he knows that here he is respected."
Rooney is only four goals short of breaking Sir Bobby Charlton's all-time scoring record for Man Utd, but has found the back of the net just once in his last 13 outings for club and country.