Rooney has endured a torrid few weeks on both the domestic and international stage, having been dropped from the Red Devils starting line-up for the last two Premier League matches.
The 30-year-old was then booed in England's 2-0 World Cup qualifying win over Malta by sections of the Wembley crowd before being demoted to the bench for the match in Slovenia.
A huge debate still rumbles on to what is the captain's best position with some saying the number 10 role whilst others believe a deep-lying midfield place suits him better.
Mourinho, who is expected to keep Rooney out of the starting line-up for Monday's trip to Liverpool, is adamant that he will still get the respect he has always done when pulling on the famous red shirt.
"He was not booed by Man United fans," he said. "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."