I haven't studied this much, but a super cursory review shows me that research doesnt look complete or conclusive, and that this "99%" statistic is being used out of context to scare people in a disingenuous way.

We don't hear what the incidence of CTE is among the population at large, or among athletes of other sports, or among those who didn't specifically suspaectvthey had it.

What we do know is that regardless of CTE a person who plays in the NFL is significantly less likely to kill himself or someone else. That means that even if one risk factor for violence were increased it is probably more offset by other beneficial factors (higher income, better access to physical/mental healthcare, higher life satisfaction, getting out of the ghetto, etc.)

Clearly lots more research is needed, but it looks like the benefits of playing in the NFL far outweigh the detriments.