After reading Freakonomics, you can't help but use some of the ideas on it to see the world from a different point-of-view. Let me explain.
The Freakonomics book revolves around the idea that people are motivated by incentives, be they financial (money and similar), moral (the set of rules you impose over yourself) or social (the set of rules society imposes over you). The Humble Bundle presents an interesting example where those three types of incentives come into play.
The Humble Bundle says you can price the games as you want. That means you have to value how much you appreciate those games and pay accordingly, but that's not entirely true - there's a moral incentive in helping charity and indie devs that come with the bundle purchase. It's basically a trade between money and the "feel good" sensation. So there'll be people who'll pay $40, there'll be people who'll pay $10 (as myself) and there'll be people who'll pay a penny. The amount you give to the HIB says much about how one perceives the value of the moral incentives involved. One may think it's really important to support charity and indie games, one may give the bundle what he can and one can simply not give a s***.
And there's a third incentive here - the social one. When Notch (the Minecraft creator) pays $4000 for the games (some of them he already owned, mind you), the social incentives comes into play, since he wants to be recognized as an indie dev who hit jackpot but doesn't forgets his roots and cares about his fellows. When he gives away the most popular indie game of recent history for free (even for a few weeks), it's both to help the bundle and to promote himself as a samaritan. It'd be naive to fool ourselves thinking that he's a saint or an exploiter, but he's no doubt pushing some of the Minecraft popularity onto the bundle while promoting his own figure. Jonathan Blow (of Braid fame) is doing the same (@witnessgame donated $2718), except Braid was sold on the first Bundle.
As for the ones who publicized that they paid only a cent, they're either trolling liars, naive children or amoral people, and I agree with the overall bashing.