Russo being dumb is nothing new.*
What works against the truth getting out there is all the false information the league put out there in the beginning and that you need to think a little to understand what happened/didn't happen. Combine that with people needing to admit their initial reaction was wrong and you've got a lot of resistance to changing opinions.
As for why the league would go after Brady, he's an easy target. Many fans have a built-in bias against his team, he was never the media darling that Peyton Manning is, and, more importantly, the NFL really thought they had him. Punishing Brady allows the league to show they don't play favorites and rehabilitates Goodell's image. The problem is, the league was ignorant of the IGL and decided to go after an innocent man. When the first inkling that they might be wrong crept in, they fully committed to framing Brady instead of backing off.
*I swear this story is true: I listened to a lot of WFAN in the 90s. Without cable, they were my #1 source for sports news. In the early 90s, there was a boating accident where several pitchers for the Cleveland Indians were injured, one fatally. Francesca and Russo were able to talk to someone from the local police (which seems surreal, looking back on it) who was at the scene. The police officer said the throttle in the boat was pushed all the way forward. After hearing that, Russo's question was "The throttle, does that have to do with the speed of the boat?"