You misunderstand. The KKK does charitable things as well. Doesn't change the fact that the ideology is flawed and fosters discrimination.
I suggest you look at the things the church has done when it had all the power. They burned women for being witches, because witchcraft was seen as the devils work. They skipped the step where they ask themselves if the devil is real. They covered the feet of non-believers in fat and roasted them. (The fat helped the nerve endings last longer) Once these non-believers succumbed to the pain and accepted God, they killed them immediately before they could backslide, for the benefit of their soul. Now, if these people had admitted they can not prove a soul, that it is merely a belief they prefer, would they then be able to find the ability to do these horrible things to people? I could fill this entire thread with examples of people committing heinous acts against their fellow man due to some belief they can't even begin to substantiate. If the church had it's way, there would be no tolerance for middle ground, no tolerance for non-belief.
Sophistication has eliminated potential for some of the most terrible acts, but we still see plenty of examples of a false and unproven ideology causing people to have ill-will towards their fellow man. This is my criticism of the church, irresponsibility, arrogance, and hypocrisy. (hypocrisy meaning, being critical of others and not yourself). The good that comes from the churches ideology is not unique to the church, it is not necessarily. Atheists are capable of being just a charitable and for near identical reasons.
As you say, you have never personally seen an atheist help. That doesn't mean there isn't evidence of it that you yourself can view if you look. Denying that atheists can be charitable simply because you have no personally witnessed it is an example of bigotry. You are ignoring solid evidence and logic based arguments in favor of preserving your prejudice, and using a disingenuous reason to back it up. I can tell by your words that you are smart enough to realize that seeing an atheist help personally is an unreasonable qualification for believing they never help at all. I also doesn't seem that hard of a concept to understand that placing good acts and bad acts on a scale and weighing them lends any credence to the ideology behind them. We call that sort of thinking an appeal to final consequences. The idea that we can believe something because good things happen if we do. Not only is it a false idea (bad things happen as well) but it does nothing to speak to the truth value of the belief.