I could be wrong, but I don't remember there being much if any talk about the Patriots running up the score until spygate changed the team's basic narrative. After that, continuing to cast the Pats as the sports-movie villains was just to expedient to deviate from.
And since in sports the conventional wisdom is defined by determinism, the fact that the Patriots suffered a huge upset and failed to go 19-0, of course everything they did during that season simply has to have been wrong. Meanwhile, Couglin goes from having the reputation as an unnecessarily rigid authoritarian to a tough-but-fair coach who can instill discipline because he's won his team's respect.
On a smaller scale, the deterministic fallacy explains why nobody noticed the Giants attempt to run up the score because it didn't work -- they didn't actually manage to score. And since JPP ended up being fine, and didn't even leave the game, nobody's going to talk about it.