Science is a business in the service of global capitalism. Truth hurts.
I will give you the MacArthur foundation and certain other non-profits. But most non-profits are also operated by the corporatocratic elite, like everything else on this planet.
It would be ideal if science were "funded" (read: controlled) by the public in the interest of the public good, but in reality it is controlled by the corporatocracy.
Is Goldman Sachs "funded" by the government or is the government "funded" by Goldman Sachs? The best understanding is that the government is a corporate subsidiary of Goldman Sachs, a profit-centre that Goldman Sachs invests in and controls by means of investment, and those investments reap profits.
Technically you could say that GS is funded by taxpayers, but funding implies both investment and control. So it's more accurate to say that GS funds the government, because this makes it clear where the locus of control is. Citizens are indentured servants that pay tribute to GS via taxes. Academics are indentured servants that receive money and position in exchange for their services to the subsidiary of GS called NSF.
Having said that, I think many foundations are genuinely independent of GS control, but they still can't be said to be funded by the public for the public. They are just altruistic private parties as opposed to the megalithic non-altruistic faction that is the corporatocracy.