Over the years I've done a bit of working with homelessness charities and even took a few homeless people into my home but it never occurred to me to start an atheist program to help the homeless. Some folks in Austin Texas are doing just that.
Check out their public service announcement video.
You can find their website at AHH - Atheists Helping the Homeless.
For suggestions some on what you can do to help the homeless, check out the links below written by formerly homeless person and atheist, yours truly.
From Your Hand to the Homeless - a list of easy to carry and very inexpensive things that would be appreciated by homeless people near you.
How You Can Help the Homeless Without Spending a Dime - a list of ways you can help homeless people in your community without spending any money.
What to Buy if You are Homeless - a list of items many homeless people could find truly life-changing plus some food for thought.