Yes, I think that atheist foundations should be given government funding just as other religious groups are. I believe that atheism is a valid religion. It may be very different from other religions, but it's still a lot of individuals belief system. Therefore, they should not be discriminated against by the government.
Atheism has no qualities of a religion, but I think that all "houses of belief", or a building where similarly minded people gather, should be treated the same under the government. So either religious groups should pay like normal, or all belief based groups whether religious or not, should be given funding and tax exemptions.
Religion, or in this case a lack thereof, is a tricky subject when it comes to governmental funding. Technically atheism isn't a religion, but in today's world of political correctness, it is only fair to extend funding to those of differing viewpoints. The total funding should also be considered comparable to that of religious organizations as well.
I think that if you are going to give religious groups government funding, then any kind of an organization that is similar should be given an equal chance and an equal amount of funding. What we want in the world is a level playing field, and this would provide that.
If Atheists could form non-taxed organizations, they, too can provide for the poor. Anything a Theist can door for charity, an Atheist can do, too! They should also have tax free organizations so it's fair. Atheists will get more respect, when they can be in a position to help others like Religious organizations can.
Athiests can't argue church and state separation between schools, churches, and government places and receive government funding as then, the government would de facto be persecuting religion which is against the founding principles. So no, in this case people who persecute others based on religion cannot nor should not receive government funding to persecute others.
Atheism is not a religion. They should not be given any money, because they don't support anything or anyone except themselves. They don't believe in anything, and aren't organized, they don't have Churches, and they don't hold events. Why should the government fund single persons? It's wrong. If they were to actually set up a foundation, maybe, but they are single people with no belief.
There is this thing called the separation of church and state that prohibits the government from providing any type of assistance to religious entities. That is why Catholic schools cannot redeem educational vouchers, and why they don't receive any federal or state funding. Atheists are a pseudo religion in the sense that they try to convert people. But are not really considered a religion under tax guidelines. But they should not get funding to preach.