The attacker returned to Old Trafford today for the first time since leaving the club in the summer but his Everton side were hammered 4-0 by Mourinho's men.
Rooney was substituted with eight minutes remaining and watched his side concede three late goals while he was on the bench.
And Mourinho praised his side's fans for their respect and is confident Rooney will be back in some capacity at Old Trafford in the future.
"I didn't need to ask," Mourinho said of the generous reception given to Rooney.
"It is the nature of English fans and big clubs when a player is big in the club and has an important part of the club's history.
"I think every club in England has that.
"I can only speak about Stamford Bridge and Old Trafford, and in both stadiums when you have former players, the reception is normally phenomenal.
"He is at home and one day I believe he will be back home."
The former United captain spent 13 years in Manchester and is the all-time leading goalscorer at the club.
Victory over Everton saw United go level on points, goal difference and goals scored with Manchester City at the top of the Premier League.
United take on Burton in midweek, while Rooney's Everton welcome Sunderland to Goodison Park.
