Well now the NFL has a problem. This will spark a big reaction from the fans. Boycotts, protests... for and against the NFL, I wouldn't be surprised to see both. But most importantly the everyday fan who tunes in to see a game and not a political controversy will stop tuning in. Viewership numbers will continue to fall, the League will start to see a drop in game attendance (ticket sales will stay good for a while, but people will stop going), and they'll start to see a drop in merchandise sales.
Goodell could have stepped on this and put a stop to it last year, when it was a few isolated players. Now it's too big to step on. At the end of the year the owners will take a look at the results, and if they have any sense Goodell will be removed as commissioner. If they don't remove him before next season, they'll remove him after next season, because if they don't remove him then next season will only be worse. The only way for the League to get out of this is to remove Goodell and replace him with a hard-ass who will restore order with fines and suspensions.
But I expect it to get worse before the owners react.