Rooney, 30, has only scored two goals in his last 18 club games and failed to find the net against League One Northampton Town on Wednesday while in one online poll, 99 per cent of supporters voted for him to be dropped.
But while United had lost their previous three games, Mourinho has said Rooney cannot be made a scapegoat as he claimed the forward had begun the season well.
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“We are a team, we are not Wayne Rooney,” he said. “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.
“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.”
Mourinho also renewed his attack on his critics by implying they had accused him of being the worst manager in football history.
The Portuguese had hit out at “football Einsteins” following Wednesday’s 3-1 League Cup win at Northampton, highlighting what he felt was an overreaction to his side’s run of three successive defeats.
Mourinho's Chelsea won the division in both 2005 and 2006, putting him in a select group with Alex Ferguson.
“History says that not many teams in Premier League history did that,” Mourinho said. “One was Man United, another one was some team managed by the worst manager in the history of football.”
Mourinho argued he had elevated expectations at Old Trafford, both with his ambition and his track record, suggesting the reaction to recent setbacks is a consequence of high aims.
“I’ve always said since Day 1 that my title ambitions are a motivational factor, a way of living,” he said. “I don’t understand to be in this club and give a different message but I knew and I admitted immediately that was a very risky approach.”
Mourinho also renewed his attack on what he sees as his pseudo-intellectual accusers, while suggesting they are lesser minds, profiting from his struggles.
“The Einsteins can’t coach, be on the bench or win matches,” he said. “They can speak, write and criticise work of other people. But I am a good man, a man of goodwill. I do lots of charity work. I am helping so many people. Why not also help feed the Einsteins?”
Mourinho argued he can cope with their comments, adding: “I’m a lucky guy. The only thing that upsets me is the kind of criticism to my players, because I love to protect them.”
While Mourinho has found fault with Luke Shaw, Jesse Lingard and Henrikh Mkhitaryan in public, he said: “It’s a learning process. When you make an individual mistake you have to learn, to learn what that means for a team that works during the week with a game-plan.
“You can be punished by that. We were punished by other people’s mistakes. The critic is part of the evolution, part of the process.”
While Anthony Martial is back in training after being injured in the 3-1 defeat at Watford, Mourinho has confirmed he is not ready to return this weekend. “It is not concussion,” he said. “He is out because of contusion in the calf and ankle area.”
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