Yes. Donations submitted via GreatNonprofits are processed by Stripe, who charges the following fees:
2.2% + $.30 for non-American Express transactions (added +1% for all international card payments)
3.5% for all American Express transactions
The donations are disbursed to the nonprofits via check by JustGive, who charges a fee of 2.2% per transaction.
GreatNonprofits does not profit from the fees.