They're tax exempt. If they want to throw off the yoke of so-called authoritarianism, they're free to reincorporate as public benefit corporations and pay taxes on all the capital they've been hoarding.
Seems like the public benefit is clear.
The benefit provided by a non-profit need not be available to all.
In fact, they are allowed to be extremely exclusive.
Institutions, as legal entities, are created by government regulations. In the absence of such regulations, all organizations would be based on voluntary contracts between private individuals. And the people forming the organization, regardless of whether you call them members, shareholders, or trustees, would ultimately be fully responsible for the actions of the organization.
Your reply is reductive: Stanford is not some run-of-the-mill LLC - they have a charter legislated into state law, granting privileges not given(!) to most other self-organized groups in the state. Saying this is not authoritarian - that's just stating historical fact.
You and a few billionaire friends can't incorporate, buy land and automatically have the legal cover that Stanford has; so no, Stanford has no right to exist in it's current, highly privileged form