Typical credit card fees are 2.9% + 30c. Assuming that they have regular fees at not non-profit rates(which tend to be lower), it would make their average donation amount to be around $7.14
With that many transactions they should be able to negotiate a lower fee than that. My company did a bit over 4 million in CC transactions last year and our rate is 1.9% and I believe the flat rate per transaction is 25 cents.
Source: 48995/689239 = (x*.029+.30)/x