Yes, they're not necessarily charities, but _in general_ they pay much lower than for-profit organizations.
To the degree that this is true, my impression is that it's due to poor fundraising departments at those organizations, which appears common enough to be a stereotype. "Nonprofit" really only affects how an organization's taxes are reported, all in all.
Charity also doesn't mean zero salary, does it?
It doesn't, but it does tend to mean heavily reduced salary because part of the employees compensation is the warm fuzzies they get.
That seems to be the case for openAI, since the compensation was lower than other offers.