The whole point of the humblebundles is for the indies to get their games into as many hands as possible.
Doing it for charity gets more sales, and good rep for supporting a good cause.
Having excess games is exactly the point.
They want you to share, to spread the goodwill.
A fantastic marketing tool if I ever did see one!
(Because no one gets to be the bad guy! Well... execept for pirates! XD
And it helps these companies in the long-term as they have more funding, but also a better position in which to sell their new games)
EDIT: In fact another interesting thing to note is the fact that most of the games are fairly old or really new.
It would make sense for the old devs, as the sales for their games may have slowed, and this gives them a much needed sales boost, but it also helps out newer devs.
Think about Voxatron for a second.
The game has a bizarre concept and image which may not sell all that great.
So when bundled with Gish and the FANTASTIC Binding of Isaac, establshed games, it helps convince more people to buy.
(As they can normally just gift those to their friends if they already have it, or be able to jump in if they didn't)