Why do atheists care?

I sincerely hope I can elicit a response from Gilbert Shapiro on two issues: (“Prayer ruling not based on merit,” Yuma Sun, January 5, 2012). First of all, with regard to the separation of church and state in the constitution, if the framers were so adamantly opposed to prayer and the practice of religion on government property, why do they open both the senate and the house with a word of prayer every morning?  Why have we established clerics not just in the two houses of government, but also in the pentagon in order to “meet the spiritual needs” of those working in there”?  

From the time the capitol was established until long after the reconstruction period, religious services representing a variety of beliefs were held in the capitol building every Sunday morning.  It was Jefferson who wrote the famous letter containing the "wall of separation between church and state" phrase, but Jefferson himself attended those Sunday morning services.  He also wrote a version of the New Testament that, until about 1917, was distributed to every freshman class of representatives and senators. 

The framers assiduously avoided establishing a religion, but they believed profoundly that we were endowed by our “Creator with certain unalienable Rights.”  The justification of the Declaration of Independence is that no government should have the power to violate those rights because, and I repeat, “they were endowed by our Creator.” In time of crisis they called for days of prayer and fasting. They believed that without our reliance on Devine providence, this great country would not survive. (http://coraleeannmoen.blogspot.com/2011/07/were-our-founders-men-of-faith-based.html). 

Perhaps Article XX of the Arizona constitution could be interpreted as directly prohibiting prayer at the State Capitol, but that leads to me to the second issue that I sincerely hope you will clarify.  Why do atheists care?

 It does takes a little time to say a prayer, but those congressmen and women waste a whole lot of time on a lot of foolishness. I doubt that there is much of an investment of capital and certainly not as much as the $2,351 they spent underwriting the production of “Abraham Lincoln’s Big, Gay Dance Party.”

I don’t think it’s really a matter of time or money, so again I don’t understand.  Why do they care?  A Google search suggested it was because atheists are not allowed in Boy Scouts.  I didn’t know that.  Some felt that religious people “are intolerant, hate filled, bigoted.”

 Many of them expressed their fear of religious wars, citing the millions murdered over the years in the name of one religion or another.  Interesting because my reading of history tells me that perhaps 100 times as many have been killed by atheist regimes,  the Third Reich, by Stalinist Soviet Union, Poll Pot, Communist China.   

Again the question:  Really, why do they care?   Were I an atheist, I am pretty sure I would just sit back and giggle at the silliness of it all. Let them waste their time sitting in uncomfortable pews and singing hymns.  Why does our prayer make them so uncomfortable?