Actually, they believe football players are contracting ALS and an ALS-like disease, and that the protein they're finding on the spine is caused by repeated head trauma. I realize it's a reverse study, but it still shows that football players are significantly more likely to contract an ALS-like condition. Obviously, that does not rule out other factors, but it implies causation. Chronic encepalopathy has been linked pretty conclusively, and the brains of football players that have been studied have produced scary results.
Head Trauma Linked to ALS-Like Disease | BU Today | Boston University
Still, you make good points, and I mostly agree with them. I think there are a lot of people who have posted in this thread that are simply bitter that football players make so much money, and have a "they deserve whatever they get" mentality. I can't get on board with that. You're right that the science is not all there yet, but enough science is (and has been for some time) in place to mandate rule changes like the ones we are finally seeing and more. The fact that it took the NFL this long to react is where I think liability will attach, if not from simply being in the best position to discover these issues.