From my point of view the problem with atheism is partly simply a matter of vocabulary (or semantics, for those of you who like Greek roots), which in turn masks deeper problems.
As we were reminded of recently by Pope Benedict XVI's statement that non-Catholics worship false gods, a variety of religious groups treat all outsiders as atheists or unbelievers. I believe the terms God and god have many definitions (sometime multiple ones even within a single religion); they are ambiguous. A lot of religious argumentation (and mass murder) hides behind the ambiguities. [For more detail see: God, A Confusing Concept] Since atheism is defined as not believing in God, that begs the question of exactly what you don't believe in, and what you do believe in.
Define God in this way: that which encompasses all that is real. In effect this equates god with Nature (in the sense of all of the natural universe), and suddenly you might say I am not an atheist, but a theist of the 18th century enlightenment sort. But define God in the way any major religion defines it today, and I am back in the atheist category. For shallow people that may be all they need to know about me, but in fact atheists vary greatly (which I suppose makes us susceptible to natural selection, and evolution).
Take Joseph Stalin, a major 20th century atheist. Uncle Joe is a big embarrassment to most modern atheists, but in the 1930's most of the world's atheists were also Marxists-Leninists and loved Stalin. Then we all found out how he killed lots of people, mostly people who belonged to his own Communist Party of the U.S.S.R. He may even have killed more atheists than that most Catholic of dictators, Adolf Hitler did; it depends on who you let do the counting.
So some atheists have tried to exclude Stalin from our fold by saying that Marxism-Leninism with its philosophy of Dialectical Materialism is actually a religion. I can't buy that argument. There is nothing about atheism in itself that makes a person good. Religions are systems of false beliefs, but simply rejecting certain false beliefs does not make you a good person. Stalin was paranoid and cruel, two human traits that are a bad combination no matter what your theological or philosophical beliefs. For factual confirmation, note that there are plenty of other cold blooded mass murders who were atheists. The common denominator of mass murder is usually political or military power, not religion or philosophy.
Many atheists have worked on the issue of an ethical basis for atheism. I think a wise human is ethical, and can develop or subscribe to an ethical system, but I think any such system should work for any human being. To some extent major religions have caught on precisely because they promote ethical behavior. Societies with a high percentage of people trying to behave ethically tend to do better than societies lacking a culture of ethics. That is why if you convene a committee of atheists, Christians, Buddhists, and Moslems (or any other religions) and stick to ethical questions, it is not that hard to come to agreements.
The same is true of atheism. To the extent that atheists are known to be strong on ethics, our reputation will rise. To the extent atheism becomes an excuse for unethical behavior, it will be condemned.
Ethics is part of my Natural Liberation Philosophy project. That is one reason I comment a great deal upon politics and governance. Ethical questions get trickier when you start trying to apply them to real world situations involving large numbers of diverse people. Systems of law may encode ethics, but they more often encode power relationships. Studying them, discussing them, a student can learn much about ethics in the real world.
If you were raised religious and are in the process of realizing you are an atheist and there are a lot of us alive in the world today, congratulations. Clarify the ethical views you were taught by your religion. Don't throw them out, build them better.