Nonprofits still have to "make a profit" on the services they provide if they want to be a going concern. Unless you've got some big project to dump it into, it goes into an endowment for "a rainy day". Which then starts looking for places to park that money.

Some of the biggest nonprofits also have the biggest endowments and/or asset holdings - colleges/universities, hospital systems, religious leadership, etc etc.

Fundamentally, most non-profits are still run like a for-profit corporation and provide services in exchange for money, they just don't have publicly traded shares, dividends, etc. Think Harvard or hospital systems, not ACLU or Red Cross.