Can't see the fuss. Matt comes out and says what 90% of the population (outside of Manchester and Kent) were thinking and suddenly he's the bad guy. Rooney was knackered by half time and contributed little to the game thereafter.
That said, sometimes you're damned if you do and you're damned if you don't. If he had hauled Rooney off, and we'd still lost, he'd been tarred with the same brush as Graham Taylor when he hauled Lineker off for Alan Smith in 1992.