It should also be remembered just how long MS has been out of racing for. Remember Jacques Villeneuve. He was out of F1 for exactly one calendar year, from late 2003 till late 2004, and even in early 2005, he really struggled. Well off Massa's pace, and a lot of mistakes. It took him at least half of the 2005 season to get up to speed, but once he was, he got on top of the job, and on top of Massa. He carried this through into 2006, when he had some excellent performances and generally had the better of Heidfeld.
MS has been out of F1 for over 3 years, and that time out has coincided with the biggest change to the cars over a 2-3 year period since the mid-1990s. And although he drove a Ferrari last summer, it was a 2007 car fitted with slicks, which can hardly count as proper preparation for a 2009-onwards comeback. So, he came into the 2010 season completely cold, apart from a few test days in a Merc which would have felt completely alien to him. So, is it any wonder he's been out of practise? And being out of practise in F1 counts for more than most people seem to realise. Also, as Gav points out, MS is up against Rosberg, who is in the form of his career, and has risen brilliantly to the challenge of being in a new team with Michael as a teammate.
MS hasn't been going badly, he's just been going less well than Nico. And as he gets more used to the car and Merc get the car to suit him more, there's no reason why that shouldn't be able to change.