Despite the argument from some theists that the United States was founded on Christianity, the separation of church and state remains of paramount importance, not just for atheists but to protect the practice of religion from state interference as well. Unfortunately, it seems the most outspoken patriots on this issue are, ironically, the freethinkers.
Atheists care about religion because religion is not some innocuous or mostly-benevolent force in society. Quite the contrary. Religion infringes upon the daily lives of all citizens, whether or not they believe. Churches are tax-exempt, yet they consume as much, if not more of public-funded resources. Time has clearly shown religion to be a significant factor in war, murder, suppression of scientific progress and humanitarian aid, and oppression of women, minorities and others with different beliefs.
Religion is "in our face"
Some believe a person's spiritual beliefs are private and personal and those people don't raise the ire of non-theists, but there's a huge amount of pro-religious propaganda that permeates everyday life. From the seemingly innocuous "God bless you" when you sneeze, to pro-life bumper stickers, daily affirmations, religious billboards, churches every few blocks, blinking religious signs, faith-based initiatives and more. It's rare to walk anywhere in public and not see some religious advertisement every few moments. Imagine if the cause of non-belief were promoted to even one hundredth this degree? Theists would be totally outraged. Yet if an atheist decides to react to the overwhelming pro-religion propaganda that's in his face on a daily basis, he's labeled as "militant", "intolerant" and "extremist." If you promote your superstitious beliefs in a public space, it's only fair that we have a right to respond to them.
Many taxpayer/government-funded institutions such as the Boy Scouts actively discriminate against non-believers.
Many civic groups, such as the Masons, refuse membership to atheists. They allow their members to believe in a wide variety of superstitious, mythological entities from Allah to Yahweh, but if you reject all that, you are not welcome.
"No, I don't know that atheists should be considered as citizens, nor should they be considered patriots. This is one nation under God." -- George H. Bush, August 27, 1987
Religion imposes its own arbitrary moral values in the form of laws restricting peoples' freedom
Religiously-motivated "blue laws" restrict what all people can do on certain days. It seems inappropriate to tell store owners they can't sell certain products on a certain day of the week.
In some areas of the country, and specifically outside the United States, it is illegal or dangerous to open your business on Saturday or Sunday, where such days may be considered holy days based on local mythology.
In many jurisdictions, the sale of alcohol is prohibited. The motivation behind these "dry counties" is based on religion. And in many other areas, you cannot purchase alcohol or other goods on Sunday.
Abortion is illegal in many areas of the country, even though many other forms of killing of creatures is often celebrated. This is also religiously motivated and inconsistent.
Atheists are forced to subsidize religion
Churches don't pay taxes. This isn't fair. This increases the overall tax burden for everybody else, and ironically churches are the last institutions that need financial support from the government.
Religion is promoted throughout a number of inappropriate, secular mediums, from being stamped on money to embedded into daily pledges expressed by students.
George W. Bush has carried this injustice even further by implementing an Office of Faith-Based Initiatives in government and taking even more taxpayer dollars and giving it to church groups.
Religion curtails freedom of speech and freedom of expression
Even moderate theists who respect the separation of church and state, help protect the extremist factions by not allowing religious debate in the public sector; a show such as Richard Dawkins' "The Root of All Evil?" would never be shown on network television in America.
Religion is actively and aggressively promoting war, conflict, oppression and prejudice
Many religions actively promote racism, sexism, even slavery and terrorist activities
The Sept. 11th attacks on the United States could not have been perpetrated had the attackers not been motivated by religion and its promise of rewards for noble sacrifices like suicide bombing
Religion stifles progress in all areas of science and society
Religious ideology is behind efforts to curtail advances in stem cell research, perhaps one of the most promising medical fields in our lifetime, capable of curing many diseases
Catholics in Africa are actively discouraging condom use, in an area where AIDS is out of control, and therefore directly contributing to the spread of this deadly disease
One of the best presentations on this subject is by an Internet activist who goes by the name "Imrational" on YouTube:
What about moderate/liberal theists/theism?
Many people argue that atheists pick on all theists when the fundamentalist/extremist ones are mostly at fault and the majority of theists are more benign and beneficial to society.
This is wrong. ALL theists and all theism is harmful and destructive. The points outlined above are not specific to fundamentalist extremists. They are common among virtually all theistic denominations.
The truth is, moderate theists are the most destructive, because they provide the cover (and the breeding ground) for the fundamentalists. They are the major force that will not allow open and honest debate on theism to exist in the public mainstream media. There are many great documentaries on science and theology that will never air in the United States because theists, even moderate and liberal ones, would not tolerate such discussion. This is because, theism really doesn't have much of a legitimate, rational leg to stand on. The very fact that all theists would rather not have their beliefs critiqued, further underlines the reality that their beliefs are most likely, not rational, and not able to be defended against in an open forum.
For this reason, Atheists can't pick-and-choose certain factions of fundamentalists to rail against. The truth is, all theists, from extremists to liberals are part of the same deluded group, creating the same problems for our society, and it would be intellectually dishonest to claim otherwise.
Another great presentation on this issue is from Sam Harris. Sam goes beyond the basics to explain why even moderate and liberal theists should be considered a threat to freedom, science, rationality and peace: