He returned from intentional duty earlier in the week where he was booed by sections of the crowd at Wembley Stadium against Malta.
Rooney was then left out of interim manager Gareth Southgate’s XI in Slovenia.
Speaking about his captain, Mourinho claims Rooney feels at home at Old Trafford.
“He was not booed by Man United fans,” Mourinho 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.”
Reports suggest Mourinho is set to leave Rooney out of the starting XI against Liverpool on Monday night.
However, even if this is the case, there is no reason to boo a player of your team, especially the captain of your squad just because of a rough patch of form.
Rooney scored the winner in the league last year at Anfield and will be hoping for a chance to prove himself on the main stage once again.