By non-profits I mean organizations like YMCA, the Rotary, Civil War historians, etc. If you are truly non-profit like these guys, then .org would be a good fit and may be preferable.
Free sites on the internet (like hotscripts, and even Namepros) usually still aim to profit from their activities via other means (like advertising, membership upgrades, donations, etc.). Hence such sites usually opt for the .com.
Still, if your non-profit is going to be popular someday, perhaps regging the .com as well wouldn't be a bad idea. Then just forward the .com to the .org so you don't lose traffic.