The term "not-for-profit" is almost meaningless here. They are not a charitable organization or advocating the social cause of "helping people invest". Vanguard makes profit. They probably make a crap-ton of profit. In fact, that's their main goal - to make as much money as possible. The caveat here is they don't have shareholders to report to, nor are they obligated to publicly report their financial statements. The top dogs at Vanguard probably make insane amounts of money all the while being "not-for-profit"... and nobody really knows because this stuff is private.
And I say this as a Vanguard customer for over a decade now, and I will probably continue to purchase funds from them for many reasons. But don't be fooled by thinking that they are doing some sort of public service by being "not-for-profit".