If the Patriots and their fans wanted the benefit of the doubt when ANYTHING shady even looks like it MIGHT be going on, they shouldn't have gotten busted for Spygate and been forced to pay the biggest fine and penalty for cheating in the history of professional sports. Tell me that others did it too and that it wasn't a big deal, but in the end, if it didn't help they wouldn't have done it and if it was wrong they wouldn't have paid the price they did.
It's been anything but a model franchise and skepticism by everyone else is the price you pay when you get caught.
The NFL was always going to have a hard time proving anything. My best guess at this point is that the Patriots do what they do to the balls knowing full well they end up lower than the legal limits and that's what Tom likes. They're detailed enough with how they plan things out that it's insulting for them to say they don't monitor that stuff. Can it be proven? Of course not, so they're safe from that, and it's looking less and less likely that anyone physically did anything to the balls. But all of this is probably going to result in rule changes about how balls are prepared and tested before (and during) the game, that's almost a certainty.
Is that intent to get around the rules? Who knows, everyone will judge that differently and if they get in trouble with the NFL, that's probably what it'll be about. And it doesn't matter if others do it, it matters who got caught doing it. But that's what the Patriots do... they push the envelope any way they can to get an advantage, and some (especially players it seems if pregame shows are any indication) feel it's a shady way to operate a franchise.
In the eyes of their fans, Bill and Brady can do no wrong and if I were a fan of theirs, I'd probably see it that way too. But public perception is very different.