Keep in mind that they will only take a payment processing fee, unlike other services that charge a cut from the payment in order to pay for their services, or at least that is what it says for now.
How are those different exactly?
a cut from the payment in order to pay for their services = additional fee on top on payment processing fee to cover operational expenses, employee salaries etc.
The second may or may not be a loss leader, but it will contribute something in revenue for the business to stay afloat.
Github already has the bills paid by paid GitHub accounts. So adding this is simply another feature and the only new real cost to this feature is credit card processing fees. If there are other costs (extra employees, etc.,) that could be counted as a marketing expense.