It's possible that HB doesn't want to be liable for the conversion of BTC to USD, and therefore the two parties are unable to come to an agreement as to how the royalties and compensation works for BTC sales. In the absence of an agreement on how to process BTC, it's easiest to simply not accept BTC for all parties.

That sounds unlikely to me, since Coinbase and the other processors promise to accept a price in USD and give you exactly that price, abstracting payment from you completely...

Don't they use a bitcoin payment processor like bitpay or coinbase which handles conversion?

Humble Bundle uses Coinbase, but maybe they don't convert it to USD.