Truth be told I think the Patriots are getting jobbed. I think this whole issue is so minor that teams just consider it part of the game. I know that Pats/Sea Superbowl is an unpopular one and SB ticket sales were tracking at 12% below average before this and now they're tracking at over 10% above.
While I do think the Patriots skirt the rules all the time, this all strikes me as something the league knew about, something that was never considered a big deal, and something the league decided to blow out of proportion out of nowhere to increase drama and viewership for the bowl.
Kudos to them, it worked. This is probably the largest media coverage of football during the 2 off weeks before the bowl in NFL history.