It happens every year, in every sport. From steroids, to stealing signs, to crowd noise, to deflated balls. I'm not saying it's right, but it's an unfortunate part of competition that will never go away.
Pittsburgh got caught with underdeflated balls last year, remember? No? That's because the NFL didn't want another over dramatic black eye on an already blemished league.
When you're arguably the greatest dynasty in sports history, people will whine and cry every chance they get to take you down. It happens with officiating too. There are bad calls in EVERY game, but one goes in the Pats favor and people flip out.