I think I need to set a few things straight about Atheists and correct a few misconceptions.
First, there are 'types' of atheist. We appreciate the irony of that (it has a sectarian feel to it), but we also appreciate that its part of human nature. These can be divided into two loose categories:-
1. Agnostics - people that neither believe nor disbelieve in God. Although they would certainly be amenable to new evidence proving the problem either way, they generally believe that the essential nature of a deity can neither be proved nor disproved. These form the majority of atheists.
2. Anti-theists. Atheists who live with the absolute conviction that God doesn't exist. Agnostics (like myself) would argue that this stance is somewhat dogmatic in its own right. Anti-theists are the evangelical wing of atheism and are largely responsible for all the lawsuits concerning religious expression.
My own opinion on the separation of Church and State is simply that it means the government is not allowed to sponsor any one particular religious ideology (a very good thing for anyone familiar with 17th century English history). It does not mean that government should be atheistic. Atheism and secularism are not one and the same. For all the bad press secularism gets, when it comes to a nation of many Christian denominations - all of which have at some point had violent clashes with one or more of the others in the past - secularism is far preferable to the unstable alternative of government embracing a particular Christian creed (or inventing a new one as happened in my own country).
I like it best split into three using terminology I've heard:
Agnostics, who as you said neither believe nor disbelieve, on the fence.
"Weak" atheists, who are basically based on skepticism: they reject the proposition that there are gods because there is no good evidence of their existence, just as there is no good evidence for Santa actually existing, but they realize the logical nightmare it is to to make the positive statement "There are no gods."
"Strong" atheists who flat out say "There are no gods."
And among all you will have a percentage who are evangelicals who must convince everyone they're right and fight to rid the world of those not like them, just like you have with Christians and Muslims.
Personally, I'm "weak." I do agree with the Newdow types that "Under God" shouldn't be in the pledge, nor should "In God We Trust" be on our money. But I'm a practical person, we have a lot more important issues in this country to fix right now. The wording on my money is about the least of my problems.