This is worth checking out over on Grantland, though maybe just scroll down to the conclusion:
That’s correct: Baseball players who accrued at least five qualifying seasons from 1959 through 1988 died at a higher rate than similarly experienced football players from the same time frame. The difference between the two is statistically significant and allows us to reject the null hypothesis; there is a meaningful difference between the mortality rates of baseball players and football players with careers that emulated the NIOSH criteria.
– Bill Barnwell, Grantland
I believe Bill James compared mortality rates for pitchers and hitters in his Historical Baseball Abstract, and found that hitters tended to live longer. If I remember, James suggested it’s because pitchers had more time to drink between starts. I don’t want to speculate too much (he says before speculating), but I wonder if football players do take better care of themselves in the same sort of way hitters take better care of themselves.