Yes, the controversy among players affects the NFL's money making ability, because it seems like every year there is another play in trouble for something. They are always hurting someone else, thinking they can get away with it because they are in the NFL. If people get fed up, they will stop buying tickets.
I believe that controversy among players brings negative media attention to the NFL, which can potentially cause them to lose support from fans and the public and therefore make less money. Controversial situations can also cause public relations disasters, and lead the NFL to lose a lot of money on PR trying to cover up the mess caused by issues with players.
Any individual scandal doesn't overwhelm its integral cultural significance in America and the wider world, which keeps fans hooked to games in order to stay in the know. The NFL's huge sponsorship deals remain unaffected by controversy as long as the NFL's huge fan base keeps the viewing figures high.
Despite the gruesome injuries, the macho culture and the off-field issues that have plagued the NFL, fans continue to tune into games by the millions. Controversy has done nothing to dissuade viewers from watching the NFL because the NFL remains a high-quality entertainment product. So long as the games are exciting, fans will watch and the NFL will rake in the dough.