Because given the right incentive they all have the potential to do evil.As you asked: Just a few charitable atheist organizations.
The main atheists charities being Médecins Sans Frontières, Médecins du Monde and Aide médicale internationale Which I think you will find are in every other war-torn or famine ravaged country in the world.
And theres.
Amnesty international
Center for Victims of Torture
Human Rights First (formerly Lawyers Committee for Human Rights)
Human Rights Watch
Gifts in Kind International
Action Against Hunger – USA
Food Bank for New York City (formerly Food for Survival)
Reading is Fundamental
Population Action International
Big Brothers/Big Sisters of America – N.O.
Homes For Our Troops
Sunshine Foundation
Compassion & Choices
National Alliance for Research on Schizophrenia and Depression (NARSAD)
Mental Health America (formerly National Mental Health Association)
American Foundation for Suicide Prevention
Population Connection
TAC
Plan USA
Madre
Action-aid
I R Teams
Americares
Doctorswithoutborders
PIH
Direct Relief
http://www.squidoo.com/Atheist-Charities
http://www.charitywatch.org//toprated.html#enviro
http://coreysviews.wordpress.com/2010/12/22/list-of-atheist-charities/
Hope that helps.