I have read many of the replies on this long thread, and it is difficult to respond without reading the article, which I have not done.
My first response is why would Payton be so foolish to make the comments that appear in the article (and his other comments about the Jets' offensive coordinator who was Denver's head coach last year). The only answer is arrogance.
This is what I think:
1. The NFL was right to penalize the Saints for Bountygate, but because of the ongoing class-action head-injury lawsuit, the league inflated and misrepresented what the Saints did and imposed an absurdly harsh penalty. I want to say that before Bountygate occurred, the NFL warned the Saints and other teams about bounties, and the Saints ignored the warning, which, if true, would explain in part the league's strong response. But with the ongoing class action litigation, the Bountygate allegations presented the league both with public-relations and legal challenges and with an ideal scapegoat.
2. I do not believe in conspiracies as the reason for bad officiating against the Saints. It would be impossible to keep such conspiracies quiet. And as I have said on other occasions, the disclosure of a league conspiracy to rig officiating against a particular team would be devastating to the NFL's business model and the valuation of the 32 NFL franchises. The statistical data that the Saints were so heavily penalized for so many years must be taken seriously. The only explanation I can offer is that Payton's actions and comments regarding officials angered some officials and affected their calls.
3. The NFL did put Payton on the league's competition committee, and Payton resigned. I understand the old Lyndon Johnson adage about you would rather have someone inside the tent urinating outside it than someone outside the tent urinating in it. But my point is that as a member of the committee, Payton could have raised some issues he wanted raised, if he had done so with tact and diplomacy.
4. I was at the 2018 NFL championship game. The no-call was horrendous. The the career of the official who decided not to call a penalty should have been adversely affected in some way. But overall, the game was superbly officiated, my memory is that there were few penalties against the Saints, and there was a close pass interference penalty called against the Rams in overtime, which would not have been called had there been a grand conspiracy against the Saints.
And regarding that game, the Saints would have won had they stopped the Rams in the last two minutes, they would have won had they scored a touchdown in overtime, and they could have won had they stopped the Rams in overtime after the Brees interception.
5. Gayle Benson is not a powerful owner in the league like Jerry Jones and Bob Kraft. But she seems a team player, and I would think she is better liked in league circles than her late husband, who had very rough edges. In short, I do not think the league is trying to take advantage of her.