Goodell's personal attitude on this issue has consistently put the league in a bad light. He often takes a detached and arrogant tone as he did with the news media in 2016 when he compared concussion dangers to the risks connected to "sitting on the couch." And then there was the time Goodell was caught laughing at a joke about concussions.
The second big problem the NFL has been dealing with this year is the kneeling protests over police brutality by players during the national anthem. When President Trump began bashing the NFL for not cracking down on this, it became a page one story. While many fans have rallied to support the players, some advertisers are feeling the heat for continuing to support the NFL. And there is no denying that this is happening at the same time that attendance and TV ratings are down. The NFL owners are concerned enough to have already met to try to fix this public relations problem.
Goodell flubbed this issue too, since the league once again has taken a mostly close-mouthed response to a very public debate. His options have always included working with the owners and the players union, (NFLPA), to find another time during pregame ceremonies other than the anthem to lodge a protest, etc. Instead, the problem has festered in a way a better commissioner could have avoided. And Goodell seemed to have made thing worse by simply saying "we believe the players should stand" and leaving it at that. In so doing, he looked a lot like a useless figurehead as opposed to someone worth about $50 million per year.
Remember too that we are just three years removed from Goodell's poor handling of the Ray Rice domestic abuse scandal. Many experts believed Goodell's time as commissioner was doomed then, but he somehow survived that backlash. Perhaps some of the owners who backed him them will reconsider this time.
Jones and his high-prices lawyers are hoping they will. He is clearly not the only owner who is unhappy right now. But even if this becomes one owner against the other 31, this is could very well become a civil war with a very ugly legal battle to go with it. The much easier choice is to seize the very low hanging public relations fruit by making a change in the commissioner's office.
The bottom line is Roger Goodell simply isn't worth $50 million and a private jet. And he surely isn't worth an NFL civil war. It's hard to see why so many of the league owners don't get it.
Commentary by Jake Novak, CNBC.com senior columnist. Follow him on Twitter @jakejakeny.
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