The FSF had revenue of 1.25 million in 2013. I'm not trying to comment on where it came from or where it went to. I'm only pointing out that they are not in a very similar position.
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.
As someone else pointed out 2.75%-2.9% is common, often thre is a charge per transaction too (on the order of 25cents after it's all said and done). The fee can change based on the card type (the merchant pays a higher fee on rewards cards normally...someone has to pay for rewards!) and international purchases can have additional fees. Charges backs can also bump up fees, ditto for outsourced fraud protection.
This is partly why I stopped donating to the FSF. They're dumping some amount of that money into misguided PR campaigns rather than helping out the developers trying to make free software better.
1.25 million USD is really not a lot of money at all... especially given all of the projects the FSF supports under the GNU umbrella.
If they had zero expenses other than staffers, at a very modest 65,000 USD a year that would not even cover 20 people.
The EFF, FSF are the only real "good guys" out there fighting for your techie rights every day... They could really use your donations and support (even if you don't agree 100% with all of their message).
In 2013 FSF paid $ 689,239 in salaries and, astoundingly!, $ 48,995 in credit card fees.