There is a definite east coast bias at ESPN (Eastern Sports Propaganda Network), and to worsen matters, ESPN reporting is larger part sensationalist drivel (BOOYAH!) than serious journalism.
Also, the NFL has a vested interest in the Pats performing well post-Spygate. Make no mistake. New England was caught cheating, and regardless of what Jimmy Johnson may or may not have done at one point, he never blantantly and callously disregarded a league-wide edict. The Patriots did and, in doing so, showed everyone that they are more than willing to break the rules, more than willing to cheat, if they can gain a competitive advantage. The issue here isn't so much what New England did; it's what New England's actions reveal about the character of the team.
Unfortunately for the NFL, the Patriots weren't just any organization. They're the team of the decade, the premiere franchise in the NFL, and the face of the league. If the public should discover that their Super Bowl wins were indeed tainted, the league's image would suffer.
Don't believe me?
Well, consider how the actions of a few Cowboys in the 90s affected the league's image, or how steroid use has affected baseball.
Obviously, a Patriots team that dominates, seemingly without the aid of dishonest tactics, is in the league's best interest.