At the cutover level (around $5), the micropayment fee is $0.50, whereas the standard fee would be $0.45. It's not that massive a difference. If people are donating only one dollar, then it's a wider difference (10c vs 33c), but this level of donations is neither a serious chunk of the total pool, nor the kind of donors you want to attract. One of the donors gave $0.02 - clearly meant to be a joke or a system test, and not the kind of donor you want to court.
The cutover between micropayments and regular payments is $12. At $5 the difference is $0.30 vs $0.41 (including the non-profit discount, which does change where the cutoff is slightly, but I don't know what it is). (I don't know how you calculated $0.50, but 5% of $5 is $0.25, plus $0.05 makes $0.30.) So, it also makes at least some difference even if everyone is donating $10 (which again brings us back to the "you need to know the distribution of payments and the model for the conversion funnel before you can talk about fee optimization ;P).
Thanks for the correction. Looking again, my source said £5, and I overlooked the actual currency. As for screwing up the flagfall... that's just a complete miscalculation on my part, sorry.
