If one of the principal reasons for choosing your product is an opportunity to maximise profits, then an organisation that doesn't actually have that motivation arguably derives less value from it and logically ought to be less willing to pay market price. Same applies for discounts "for academic use" etc. Price discrimination isn't just about assuming a particular entity has less funds, period.

Whilst nonprofit != charity it's also perfectly reasonable to make the value judgement that it's fair to implicitly subsidise social goals at the expense of other clients' shareholder returns. Provided no laws are being flaunted, I can offer discounts on a service I provide to people for virtually any whether its because I believe in their mission, like them on a personal level, respect their OAP or veteran status or just desperately want their money. One of my local curry houses gives discounts to Arsenal season ticket holders. Nobody should feel _obliged_ to make these concessions, but when many companies do makes sense for nonprofits to ask the question. I bet 37signals get plenty of emails from startups and small businesses asking for a dose of sympathy and lower prices too.

Sometimes, where you have a high margin business and close competitors that will discount, it makes sense to give them what they ask for too.