Yes, if you're giving enough that the credit card fees are substantial, then you should be using another payment method. At worst, mail them a check. There's nothing better for a small non-profit than to open a letter containing a large and unexpected donation check.
I can recognise, from the links in this blog and other posts on the same blog like [1], that the author is giving a double-digit percentage of their income to charity. Maybe as much as 50%.
A person earning $100,000 and giving $50,000 to charity who paid a 2.9% card fee would be giving $1450 to a credit card processor - money that could have gone to the charity had they simply done a bank transfer instead.
Of course, for many charity donors paying by credit card is fine - better a moderately efficient donation that happens than a highly efficient donation that doesn't happen because of the inconvenience barrier!
[1] https://www.jefftk.com/p/earning-to-give-transcript