Thanks for reaching out! To start, make sure you have already received your non-profit status from Stripe. They offer some incentives for non-profits, including a 2.2% rate for non-American Express transactions. You can find out more about that here:
As for the app, we unfortunately don't have a mechanism for applying discounts to the 1% fee quite yet. We would absolutely love to do that, but at the moment, Stripe doesn't offer a way for us to identify if your Stripe account is a non-profit or not. They don't expose this information to 3rd parties. Since our fee is baked into the app, we can't have it change from customer to customer.
One thing that would be helpful would be to email Stripe and let them know that you would like that information exposes with your account so that the app (Payment for Stripe) can give you discount pricing as well. Maybe if we get enough non-profits to send an email like that, we can start offering that pricing as well!