A couple of thoughts:
1) Some of the banks were forced to take the TARP so the others wouldn't look too weak competitively. Those employees are hosed for the greater good.
2) Some may have come on board to help clean things up and may have specialized IT / math skills. Their comp may have a higher variable component weighted toward attainment of personal goals so the company can maintain capital reserves. They won't be happy campers.
3) The cap is based on family AGI. So someone who's spouse makes a reasonable wage elsewhere will have their bonus confiscated, even if they make $50K.