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?
30 pennies +2.9% is what Paypal charges and is normal for many credit cards. Because of Interchange fees credit cards are at least 2% for Profit driven companies even if the Business is so large they own their own credit division or bank. With credit cards there is a perverse penalty where small businesses pay 3-8% per transactions and the large multi-national corporations drive the costs down to a little above 2% per transaction.
Bitcoin is already much better than credit cards, but has room for improvement. Payment channels will solve the 10min avg confirmation problem, blockchain bloat problem, and the micro-transaction problem.
There are already multiple payment channels for bitcoin for micro transactions ... but they tend to focus on tips now.