Fact is, it was legal during the Pats' Super Bowls. Just like how it was legal for Mike Shanahan to have a lip reader watching his opponent's coach back when Elway won the Super Bowl. Just like how it was legal for John Madden to watch his opponents' practice when he was a (Super Bowl-winning) coach. Be it breaking Carson Palmer's leg, wire-tapping locker rooms, spying on practices, pumping free agents for info about their former team or any other questionable dealings, every team has done SOMETHING. You can run down the entire list of Super Bowl-winning teams and I'd bet you'd find something that they "cheated" with. But the Pats were "acquitted" for lack of a better word by Gooddell, but even if they weren't it'd be lame to hold it against them, since that would just fall under the category of "too bad nobody else thought of it first."
But you simply can't deny that the Pats are being singled out, for whatever reason (be it that everybody hates Belichick cuz he's beaten them or the media hates him because he practically tells em to screw off). Eric Mangini is the guy who ratted out his roommate for sneaking in beer right now. All the other head-coaches are trashing him in a non-public setting (according to NFL sources). Not to mention the simple fact that when the league voted on whether or not to have defensive players use headsets, it was voted down (guess what the reason is).
But the Pats by no means got off easily. In alot of ways, the taking of a first round draft pick is the harshest thing that Goodell has done as the commisioner.