They usually take donations via credit card and need to pay the credit card fees, plus make some kind of profit.
They also do not allow for BTC payments AFAIK.
All nonprofits should occupy the bitcoin p2p currency space already, as it is even more of an obvious sector than the widespread retail adoption we are seeing. Tax write offs and all plus the potential for projects like Peace Corps, Heifer, etc of further empowerment advancement of its causes by establishing economies in the unbanked parts of the world they constantly are working in.