Humble Bundle Bitcoin miner fees?

no one?

Pretty sure the miner fees are set by your wallet provider, not by Humble Bundle itself. Also, I believe the fee may vary depending on the amount.

EDIT: I realized that I had misunderstood your question. Miner fees = transaction fees.

a penalty for trying to spend small coins(5, 10..cents) to pay a $100 bill

When you spend a small amount of bitcoin you have to pay a little extra for the transaction to be verified quickly. However in my experience even a $1 worth in bitcoin was transferred instantly without paying extra.