There is a difference between registration and filing. Tax-exempt organizations with more than $5,000 in annual gross receipts must register with the IRS, but they don't have to file the annual information report until they reach annual gross receipts of $25,000. Religious congregations have automatic Section 501(c)(3) status and are not required to register or file. Foundations of any size must register and file.
Nonprofit organizations with over $25,000 in annual gross receipts are required to file Form 990 with the IRS. Organizations that have gross receipts between $50,000 and $100,000 and less than $250,000 in total assets at the end of the year can opt to file a shorter form called Form 990-EZ. Private foundations of any size file Form 990-PF. Since some funders require Form 990, some smaller nonprofit organizations do file Form 990 even though they are not required to do so by the IRS.