I really think the major credit card companies missed a tremendous opportunity by not figuring out micropayments. They have the infrastructure to be the ones to figure this out, but they didn't.
Just drop the flat fee. Stripe is 2.9% + 30c. If they did 3% and no flat fee, then on $1 you'd get 97 cents instead of less than 70. I assume the CC companies are charging a flat fee too...unless that's just Stripe's own thing.