Rooney's performances have been under the spotlight in recent weeks, with the 30-year-old struggling to make his mark for the Red Devils in the early weeks of the 2016-17 campaign.
However, Mourinho has insisted that his team's problems, which have brought two straight Premier League defeats, go deeper than just Rooney underperforming over the last couple of weeks.
"We are a team, we are not Wayne Rooney. We all started well, we all won four matches, and we all lost three matches in a week, so that is not [just] Wayne Rooney," Mourinho told reporters.
"To be honest he did not even play against Feyenoord, so he was directly involved in the last two matches. We had a very good start to the season, better than we expected and prepared for, and we were guilty of raising the expectations of the people and then we lost three matches in a row."
Man United will attempt to return to winning ways in the Premier League when they welcome champions Leicester City to Old Trafford on Saturday afternoon.