Income reported on Form 1099-MISC is self-employment income. If you made more than $400 of self-employment income you have to pay self-employment tax, even if it's not enough to have to pay any income tax. Self-employment tax and income tax are two separate taxes, even though they are both included on your income tax return.
It makes no difference that the organization you worked for was a 501(c)(3) organization.
