I received this reply from CCS. Comments follow.
Thank you for writing to Anne Goddard and sharing your concerns. Anne was traveling when she received your email. We discussed your concern and she asked that I respond on her behalf Please know that we take your email very seriously.
There appears to be a misunderstanding which I would like to correct. When Gen Con contacted CCF about its auction, we were pleased to accept donations. However, we couldn’t lend our name for publication because our policies have specific criteria for endorsements. We were unaware that this had caused any problem or concern for Gen Con until we began receiving emails. This decision was in no way intended to be a reflection on Mr. Gygax, gaming enthusiasts or the game Dungeon and Dragons. We have the utmost respect for the gaming community and were touched by the generosity expressed through your auction. We were disappointed that we were not the recipients of the donation but we were pleased that another worthy organization benefited.
We realize this has become a topic of discussion in the gaming community and we hope you will help us by sharing this response.
The needs of children are great and we welcome your support. Should you wish to learn more we invite you to visit our website at www.christianchildrensfund.org.
Again, I thank you for taking the time to voice your concern. Your passion for gaming and your support for children are admirable.
Vice President, International Communications and Fundraising
I can understand why an organization might not want to give permission for its name to be published in an event brochure if they have no control or influence over the event. It's not a common policy, but it's not unheard of.
For example, a pet charity I'm familiar with stopped allowing itself to be listed as a recipient at most dog shows after a judging scandal at a small regional show that had been heavily advertised as "come support the (pet rescue organization). It didn't mean they opposed dog shows; they just didn't want to take a chance.
This letter seems to indicate that the nature of the convention (or what games were featured) was not a factor in their decision.