FTW I agree. Kraft is most guilty of going along to get along. Him and the owners hold the greatest blame next to Goodell himself. But as unpopular as this may be, Brady has a modicum of guilt in it too. His name carries a lot of weight. Did he rock the boat to change the system that was railroading other players? In reality most of us diehard fans are kind of guilty on this (with a big shout out exemption to Joker-Man). That's how big, how ubiquitous the game of the NFL is at this point. From the average fan to some of the most powerful, to the average to the most decent of us, precious few have bucked the trend of the NFL Titan. Think about it, how many of us took just a modicum of time to look into Bountygate or the Incognito thing or the Boys/Skins thing, and then spoke up to show support for an injustice (how many of us were Steph?)? Sure there were a few, however, there were very few. 99% of us just wanted the season to start. (huge shout out to the Joker-Man for being one guy to fly the flag of Goodell The Railroader for many many years and even enduring ridicule for it).
But I think the commissioner's office has gotten bigger than the owners expected or maybe even recognized in time. I don't see any way, deep down how most of these owners can like what they are seeing. They have to know where the trend is heading and have to know it will eventually pull into a station that it can't pull out of. But the thing is, if you are an owner and you speak out against the commissioner (even privately but certainly publicly) -- and you do not have the unquestioned support of a lot of other owners(a difficult reality) -- you are putting yourself and your franchise behind the eight ball. Goodell has shown he will use the power of his office to injure. He is even arguing on court that guilt is irrelevant - he can decide it any damn way he pleases. So as an owner why in the world would you think Goodell will not do it to you/your team? He will. So I have a suspicion that even the owners, as individuals, feel a little powerless against the commissioner, and an individual owner is definitely skittish about going counter to the commissioner.
Another possibility here is the office itself as a collective may be the issue as much as the commissioner himself(though he would have been the catalyst for it all). Take a look at government -- you can clearly see that the unwritten branch of government (the administrative branch) has power that the political leaders themselves sometimes can't constrain. So while it may not be likely, it is possible with the size of the NFL that the NFL administrative branch as a collective is so powerful the the individual figure head can't always restrain ((this thing is so out of hand for something so undeserving of this absurd attention and fight, even the seemingly implausible has to be considered as an underlying cause of this surreal reality)).