I believe some of the tension that has arisen in this dialogue may lie in a misconstruction of definition.
Atheists have a worldview that does not include a supreme being. That is not to say that they take an oppositional view to organized religion. It simply a matter of a deity not entering into their worldview. Atheists can construct moral codes on other merits and even have a spiritual understanding of the universe. The disbelief in a higher power does not exclude either of these.
Most atheists also do not have a conflict with those who believe in a supreme being. Conflict only arises when people of any religious persuasion attempt to regulate their day to day lives based on a belief system that is not their own. This could be said of any person religious or otherwise.
Now there will be some who argue that there are many atheists who openly oppose organized religion. These fall into the category of anti-theists which is another matter entirely. Anti-theists believe that organized religion has an actively negative influence on the world and are as proactive in spreading their philosophy as any religious group that practices proselytism.
All that being said, even atheists would have a problem with anti-theists when they try to impose their philosophy on those who believe in a supreme being.