The make-up of this TdF really did not suit Sagan. In previous, Tours he's locked up the green jersey by securing intermediate sprint points that were guarded by Cat climbs. The heavy climbing focus of this tour meant that the sprint points were mostly before the climbs, so there was no way to drop the traditional sprinters. Stage 7 had a more traditional layout, and Bora dropped Bennet and secured a ton of points (before the relegation), but that wasn't an option on most stages.
Also, Sagan is a marked man. They were NOT going to let him get into a breakway so he could get sprint points. In the past, he's had more margin.
That said, Sagan looked out of practice, especially early on. He was constantly picking the wrong wheel, not finding clean lines, etc. He's usually a master of that. I think the COVID restrictions really effected his TdF preparations, but the stage layout was much more suited to a traditional sprinter than in previous years.
Oh, and Wout Van Aert could absolutely own the green jersey for the next several years if he wanted. Phenomenal tour for him. He was in the mix on the sprints, and crushing it in the mountains.