Oh absolutely. This is all largely for show, but at the same time it is still leaving the ball in Rooney's court. Mourinho started the season with Rooney established in our strongest 11. Rooney didn't perform. So now Mourinho is going to start phasing him out, while still giving him the opportunities to prove he should still be in there. If Rooney can't even take those opportunities (as he didn't in this match), he'll find himself getting less and less chances, and the ones he does get will more often be in the 'lesser' match of the week rather than in with the strongest 11.
That's how I see things going over the next two months or so, and it'll be up to Rooney as to how things will end. If he doesn't perform, he's got no leg to stand on to complain when he gets dropped more and more.