The Conference is not charging for this service, but the merchant fees charged by the credit card company or the processing bank are unavoidable. The calculation depends on whether your donor gave by credit card or by ACH (from a bank account).
Card Fees = 2.60% of the donation amount plus 39 cents
ACH Fees = 0.75% of the donation amount plus 39 cents
Your donor may have opted to donate an extra percentage to help offset those fees. That additional amount is not calculated the same way, so the net amount sent to the church will most likely not be an even dollar amount.