I think people need to realize that motor sports are less sport and more business than they used to be. If Hamlin legitimately screwed up, then that is on him, though I do believe that NASCAR would have wanted Tony to win because of the "comeback" story and how exciting a last-lap pass would be. Stuff like that brings in revenue which keeps NASCAR afloat.
And like
@Dotini pointed out, Tony in the Chase means more viewership and hence more $$$. Keep in mind as well that Jeff Gordon retired last year and this is Stewart's last year. Those two are among the most popular drivers, so once they're gone, there's going to be a huge gap to fill. Only Dale Jr., and possibly Danica and Chase, are going to be the real big moneymakers until they call it quits.