Having worked for and with non-profits and governments for most of my working career and having written a ton of non-fiction, I have never proposed a fee up front, only responded to offers, and I have never seen a non-profit publish a work, without a grant, that really paid the author much more than a small stipend.

The problem with non-profits is that most of their publishing endeavors don't generate revenue for the non-profit. Unless the published work is either mandated reporting, covered by a grant or part of the non-profit's mission, the best that they can hope for is a donor to cover costs. Which does happen, but it's really rare.

Submit the proposal and see what they offer. Go from there. Don't expect to get rich but, unless the non-profit is something you support, don't take a hearty "Thank You" as payment.