It's not comparable. Messi is the greatest player of a generation, Rooney isn't even the greatest player at the club.
As I've said, it is speculation, but based on previous events. Rooney's christmas period last season (and the season before) weren't good enough in terms of attitude/performance. Then he has his worst game of the season at Swansea, and coincidentally gets an injury, seeing him through till the new year.
Rooney doesn't always start our games. See my other post, where he was dropped for the Liverpool game last season, and dropped for the Blackburn game last season, and the game against Fulham I believe this season.