You can choose where your money goes to; Publishers, Humble Tip and Global Giving's Hurricane Harvey, Irma, and Maria Relief Fund or even choose your own charity.

While it is pay what you want meaning you can pay $1 for tier 1 or giving away more than $15 for the relief fund, Bitcoin payment method requires to pay at least $2.50

As i write this, I asked Humble's comment on if they will accept Bitcoin on their store too, for now it is pure speculation and still waiting for an answer.

source: https://www.humblebundle.com/books/bitcoin-cryptocurrency-books