Once big money finds its way into a sport, LOTS of competitors, even good people, try to bend the rules - and sometimes cheat - in order to win. This happens in every sport and requires ongoing efforts to contain it to within reasonable limits. As such, penalties need to be dished out according to the severity of the offense. When careers, livelihoods, sponsorships, book deals, etc. are on the line and winning is what makes these things possible, it is inevitable that people/teams will (and DO) go to any length in order to win. Even in my "lesser" sport of table tennis, there has been tons of cheating over the years, including doping, equipment tampering, etc., from players and coaches all over the world... in some cases by friends of mine who I respect.
My own favorite baseball team, the SF Giants, had a player caught doping a couple of years ago. Of course the team, coaches, players, etc. went into full denial mode - shocked! dismayed! But, really, did the coach know about it? It sure wouldn't surprise me one bit if he did. I hate to admit that, but hey there is a LOT on the line and those immersed it it learn quickly that you can't afford to not do everything you possibly can to increase your chances of victory, however tiny. Those little things add up. Otherwise, everyone else will, and you'll end up in last place, with no career, and forgotten. The terrible truth is that nobody remembers the honorable last-place finisher. Sport becomes ruthless when money enters the picture. There is absolutely no need to build a conspiracy theory to explain anything. The Pats just got caught this time (probably/maybe).
One can only guess how much cheating is going on that we don't know about. If you're a sports fan and consider yourself ethical, you have to reconcile yourself that your favorite team(s)/athlete(s) are very likely pushing the envelope on many of the rules. Money corrupts, it just does... the Patriots are NOT unusual in this regard. If every team was kicked out for every little transgression, there wouldn't be a league left.