We charge 3.9% + $0.30 for each transaction. (For Stripe accounts outside of the US the fees may be different, both higher and lower depending on your location. Contact us for more information.) Those fees cover costs from the banks handling the transactions as well as WePay or Stripe's costs, plus a little for us to help keep the lights on.
WePay or Stripe handles all disputes and chargebacks from your donors. They will contact you directly if they need anything from you to handle these.