For those even casually acquainted with legal circles a few things shown through.
First, Tom Brady was not suddenly declared "innocent" (this was not a criminal trial anyway), the process used to determine his punishment was fatally defective, nothing more.
Second, that process was so poorly handled it defied "fundamental fairness" and let me say that you really have to screw up to miss that bar given the CBA in place at the NFL. While not expressly stated it seems clear these were not a series of mistakes. If they were ... wow ... just wow.
Third, Judge Berman's decision was akin to an AMRAAM attack on an anthill. It was a complete and utter evisceration of many of the principles in the CBA regarding punishment for players. In short, the NFL is going to have to fundamentally change directions on how they handle same. With this decision, the NFL should be on notice. This will serve as a negative to legitimate wrong doers as well, who will use the defective process to skirt appropriate punishment. That too is just as bad as using poor process on an individual who does not deserve it.
Finally, the NFL has gone after one of its best marketing assets. It has tarnished the image of the "Golden Boy of Football." Tom Brady is an ambassador for the NFL and has worked hard at that image. For the league to pursue the cause to begin with and continue it until this point (I believe they will withdraw the appeal ... and the fact they did not ask for a stay was telling too) seems completely opposite of the goals of the league which are to (a) make as much money as possible and (b) appear a wholesome lot while doing so.
Tom Brady allowed both, and the NFL in their infinite wisdom just $h!t all over him.