While 9 pennies is a hell of a lot better than 30 pennies +2.9% found with many traditional merchants your concern is somewhat valid and we should encourage lower fees for micro transactions.
Is this the formula for a credit card? That would mean that spending $0.25 would cost the merchant $0.31? Or is there another credit card formula for micro transactions?
There is an 848 page law in the US and tucked away in it somewhere it says that merchants can set a credit card minimum purchase of up to $10, as long as they treat all cards the same. It also allows the Federal Reserve to review and increase the minimum payment amount.
I don't imagine any merchant is going to let you charge any amount that would cost them more money than they would make on the transaction.