There was so much leftover bullshit from Spygate that impacted Deflategate that it's impossible to tease it all out.
In addition to above, there was this bizarre paradox that people simultaneously thought that the harshness of the Spygate penalty was proof of severe wrongdoing (and not merely the technical violation that it was), but at the same time Goodell was "soft" on Kraft because Kraft was a "shadow commissioner."
My take has always been that:
A) Goodell, new Commissioner, was overly harsh on Spygate because he wanted to set a tone of authority in the face of Belichick's disrespect for the rules;
B) Kraft, because he recognized the need to ingratiate himself to the league in light of what happened in Spygate, made it his business to be useful to Goodell, particularly in negotiating the 2011 collective bargaining agreement, for which he received the
lion's share of credit.
C) Other owners begin resenting the attention Kraft is getting, and suspicious of his closeness with Goodell, start spreading the "Shadow Commissioner" whisper campaign to play up Goodell's insecurity;
D) Goodell, in order to dispel the image of Kraft's influence, uses Deflategate to smack the Patriots again and in the process determine the actual legal lines of his own authority. This was made possible from a PR standpoint due to the lack of correction issued for the reasons behind A.
And through all of Deflategate, Kraft naively thought he would get a fair shake because he had acted in good faith toward Goodell, and served the league well, since 2008. That everyone saw he was being shivved in real time while he played softball until it was too late made it all the more infuriating.