It certainly does NOT imply or even come close to suggesting that 99% of football players will suffer from the disease.
I think he understands it better than you do.
He never said there was a 99% chance of him developing CTE.
His actions say that the chances of him developing CTE if he keeps on playing football are higher than he wants to take. If we were talking about my brain, that would be somewhere around 0.001% as an acceptable risk.
The math for anyone who has any other option in life is pretty simple: You have exactly one brain, but more than one way to make a living.
Well stop driving or using the stairs in your home then, because the actual, documented risk of brain damage for either of those activities is higher than your threshold.