When donating to charity non-believers may feel more comfortable donating to secular organizations whenever possible. There are more than you think and some you will recognize. Most of these are simply secular organizations and charities; not necessarily “atheist.” This would account for the misconception that atheists don’t give. We do. We just don’t make claims that help and service is in the name of anything other than help and service.
If you are interested in searching for various types of charities try the Charity Navigator.