You are mistaken in the fact that the majority of players have million dollar contracts. The actual truth is that the majority of football players don't make a million dollars gross in their short careers.
Edit: beat to it while I was typing.
[1] http://www.steelersdepot.com/2011/07/2011-2014-nfl-minimum-b...
Also the average salary is about $2m so you're looking at $12m gross. There's certainly a power law there, but still, an average salary of $12m careerwise is substantial.
So, rather than $12M, we should be talking about $2.4M for a median career, and that's just those who play an entire year before getting cut. Since the NFLPA is toothless most NFL "contracts" allow a player to be cut at any time for any reason and then he doesn't get any more money.
I don't think this is because the NFLPA is toothless. I think it's because the marginal value of the 53rd man on the roster over the first guy on the practice squad is not high, and it doesn't increase much as you move up. Because the NFL is such a team game, with a few major exceptions players are largely replaceable.
That's why you hear so often about guys who were sitting on the couch watching football one Sunday and playing the next. This effectively doesn't happen in, say, baseball, where the supply of guys who can hit major league pitching above the Mendoza line is quite limited. Even with a huge farm system, teams rarely have more than a few major league-caliber players who aren't actually on the roster.