Three points that I would suggest:
1) They're comparing a sample of people who, by definition, have generally superior genetics and conditioning habits, to the general population. A lot of the things that cause men to die young would also preclude them from ever having a shot at playing in the NFL. As the study notes, for example, only 126 NFL players in the sample died of heart disease, versus an expected 186. Defensive linemen were the only group who were more likely to die of heart disease than the average, but the rest of the group--even offensive linemen--were below the average to varying degrees.
2) The study includes men who played between 1959 and 1988. If you believe that the CTE problem has gotten worse in recent years, due to significant increases in player size and speed, then this study hardly debunks that. This is especially true when the study itself suggests, at least, a correlation between player size and mortality (players with a BMI >30 were twice as likely to die of heart disease).
3) The CTE/quality of life issues can't necessarily be neatly divided into one of life and death. There are a lot of players who go on to live miserable lives, post-football, on account of their diminished mental faculties, but do not actually die especially young. Quality of life is not addressed by this study.
