Why not? His pad prevented the ball from hitting it, where it otherwise would have.
I see your point though, how accurate is the system really and how can it say that the ball is or is not going to just hit the stumps.
Hokay, I grew up in an era where it was assumed that the benefit of the doubt went to the batsman (because once he was gone he was, well, gone, and the bowler always had another chance) - it did sometimes get to the stage when, say, Dickie Bird was umpiring, when nothing was ever out, but for the most part this worked equally - albeit with some poor decisions made (reference the Ashes series in 2005, for example).
Now, DRS has done many good things - its revitalised spin bowling for a start - but its primary purpose was not to change the rules, but to get rid of the shocking decisions. Now, to take Pietersen's today as an example, Hawkeye showed that, at best, the last coat of spit on the leather was brushing the very edge of the bail. Benefit of the doubt, perhaps? On the screen, you could see middle and off stumps when the ball hit him and it did not in any way look out! Strauss got a similarly poor one second dig in Abu Dhabi, when the ball *might* have been partially in line and *might* have been brushing the top of the stumps - again, that to me is a stinker, no doubt about it...