Here’s a quote from the article:
About 30 nonprofit agencies that held several accounts at Freedom, each with less than $100,000, lost money because the F.D.I.C. considers the multiple accounts of a single depositor as a single account. The Fort Greene Senior Citizens Council, for example, had 24 separate accounts totaling $316,000. The F.D.I.C. reimbursed $100,000, leaving the council with a deficit of $216,000. [emphasis added]
This isn’t meant to panic you. And I’m not a financial advisor, nor have I played one on TV.
But if you were told that your nonprofit would be FDIC insured with multiple accounts at the same bank, you may do well to check with your own financial advisors.