Dan Rooney was extremely upset with Goodell’s handling of the “probe/conclusion“ and was one of the four principal owners who privately told him so. Mara, Hunt, Wilson all expressed astonishment to Goodell actions and that because of them he alone could jeopardize the league‘s AT exemption. (new owner of NYJ Woody Johnson also was pissed, since Belichick never allowed Johnson’s management team to meet him regarding Leon Hess’s promise). After all the internal discussions revealed how those actions were on the behest of Kraft, various other principal owners, like Richardson, Davis and Jerry Jones were livid as well citing Roger was giving preferential treatment to his longtime buddy. It all hit the fan once Congress couldn’t ignore the media circus the New York Times and Boston Herald was putting on it. At that time, the League AND NFLPA all downplayed the incident for the benefit of the league itself as Senator Spector had asked Goodell to appear before a senate hearing since he stated to reporters taping had occurred retroactive to 2000. Spector wanted an explanation as to why this was ignored, and the tapes destroyed. Congress ended their purview but indirectly noted, they would keep watch.
The owners didn’t want a repeat as to what happened to MLB with the steroid scandal. They saw how the public reacted in boycotting for several years. At the time Mangini accused NE of cheating, the league was in a barfight lawsuit with Comcast/Cable distributors regarding having NFL Network not having access like ESPN on their general base packages. They knew any further negatives to the NFL could impact fans and drive them away.
Now several years later after the IND game where balls were deflated, and Marcia’s refusal to cooperate and Kraft employees going absent, the owners pushed the commissioner to appropriately punish Kraft and Brady, since Belichick was being protected by Kraft. It wasn’t a suggestion, but rather a directive.
Anti-Trust exemption is what makes the League work better than any other Sports League (with true parity) because the stupidity of one franchise can impact all the others. That’s why Al Davis had such a contentious relationship with Pete Rozzelle. He had no favorites, the League was the end product.