The concept this runs around is that most people who pirate are people who wouldn't purchase, regardless of circumstances.
Generally speaking, most of the people who paid little, or nothing, are people who wouldn't have purchased the game anyway, so very little potential profit is being lost from that sector. Furthermore, most of the games involved have been out for a while, and have already peaked, meaning their rate of sale is rapidly declining.
Meanwhile, hundreds of thousands of gamers are exposed to these games, which raises the profile of each of the studios involved. Basically, they use the collective appeal of all of the games combined to boost their studio's fame. This results in the studios having a stronger pedigree, which in turn will lead to increased sales of their future titles.
"Hey, they're the guys that had that great game in the last Bundle;
This new game could be good!"
So, by sacrificing the last little dribble of sales from their existing titles, they get to gain (relatively) massive public exposure, public goodwill, and help out charities.
The third humble bundle sold over 370,000 copies, at an average of $5.80 per sale. The total amount raised was roughly 2.2 million dollars. There were 7 studios involved, with the average consumer giving 30% of profits to the developers (these numbers gathered from Wikipedia and a variety of other sources, none of which are supremely credible). So, each studio on average made $94,000 in the space of 2 weeks.
Considering that 6 of the 7 games were over 12months old (4 were over 2 years old), which for an indie game typically means it's well past its prime, that last boost in revenue is nothing to sneer at.