The Daily Mail fabricates a lot of stuff, so one has to be careful reading their stuff.
That being said, this business of Rooney not being fit has been a constant refrain for years. Yet when he plays he seems perfectly fit, to my untrained eye. He's not apparently overweight and he runs hard the entire match. So I'm not sure how much there is to those stories.
I was shocked that he wasn't in the first XI for Madrid. Wellbeck had an excellent game behind the striker. Pundits have suggested that Rooney could have played one of the wide positions. I'm thinking that Ferguson sent out a team which he believed would be his strongest defenders.
He was right. Before the red card Madrid weren't able to launch their counter attacks and looked lost when attacking. After the red card, when Madrid were basically assured possession, he plopped Modric in the middle where he could sit and be the general of a game played at a slower pace and Madrid looked great.
Long way of saying that tactics, not fitness, might have been the issue with Rooney.