The idea that all charities regularly reject money donated as a result of events in which they have no organizing hand is utter crap, cooked up by their customer service department after the fact to answer angry emails.
Quite true and the fact that CCF isn't some sort of weird exception this general practice is evident by their working with Capital One on a percent donation credit card bearing their logo. I don't suppose they had any hand in deciding who would be approved for the card or what the APR would be, do you?
I think they might have gotten to help pick the design schemes available on the faces of the cards though. Maybe if Gen Con had offered to let them help decorate they would have taken the donation. Sure.