Luke, the facts regarding the separation of church and state in this country are clear. The idea of religion is, none the less, a very powerful one, and many people use religions terms to communicate strong feelings, even those among us who are flat-out atheists. It's a question of communications.
The fact that statues, etc, appear in various government buildings neither shows the intentions and motivations of the founders, who acted long before the statues and buildings, nor justifies the present misbehavior in attempting to dishonestly and traitorously inject religion into the government.
"In God We Trust" was introduced by another good repugnican, Joe McCarthy, during another period of national hysteria, and passed by another repugnican government.
The republicans have, for some time now, acted directly opposite the intentions and written word of the founders. George Bush (daddy) showed that this was intentional with his insulting suggestion that "atheists are neither patriots nor good americans, this is one nation under god" comments during his own campaign.
As far as the scientific method being how this country assumed power, there is absolutely no doubt or debate. That's how it happened. The tradition of understanding of secular things like gears, motors, water mills, etc, started this country to its position of world dominance, and the continued research, culminating in things like Edison's lab, Bell Labs, and the like, are how it continued and grew.
All of those people and institutions, regardless of their religious nature, had one criterion for mechanisms, that being "does it work". When this country was founded, the philosophical basis for the scientific method was in its infancy. As the method evolved, so did the work of science, including the recognition of science as primary, and religion as irrelevant, to lawmaking.
Now, we fast forward to the 1950's and 1960's, wherein many changes happened, both to the educational system (where the scientific method was effectively thrown out) and to the political system (where "scare tactics" became a way to overcome the wisdom of prior generations), and we got "in god we trust". From there, the government has attempted to push more religious issues into government policy, witness the foolish restrictions on overseas medical funds, the insistance on "only teach abstinence" (yes, it's the best way, but insisting on that is a simple denial of the medical scienc eof the matter), the legislation effectively halting stem-cell research, using a heap of quackery and nonsense to justify the claim "we have enough', and so on.
It's simple, really, we stand at a crossroads. Do we enter a new religious dark ages like the present Republicans would have us do, give up the tools that made us great, destroy our ability to defend ourselves, heal ourselves, and add value for trade in the process of giving up exactly the scientific method that made us great in the first place, or do we not do that?
That's where we stand. Your argument about "the will of the people" is exactly and precisely stating that you wish to ensure your will over minorities. In that, you are little better than the person who wants black people to move to the back of the bus. The situation really is quite similar, you know, atheists aren't very welcome in elections, atheists can't be "patriots or good americans" (the former President has said so, after all, ex cathedra), there are a variety of attacks on atheists every Sunday from pulpits, atheists are blamed by widely circulated hatemongers, along with other non-majority types like gays and wiccans, for 9/11, that being the "wrath of god" instead of the scientific conclusion, a failure of intellegence brougth about by infighting between government agencies, an infighting that was encouraged by decades of government from both sides of the aisle, and so on...
9/11 is, in some ways, an example of what happens when policy trumps the scientific method. It's a symptom, alright, of us abandoning what made us great.
Luke, you have to take your stand. Do you support the dictatorship of the majority, or do you support freedom? That's not a false dichotomy, Luke. When you say "the will of the majority" you speak the very idea that the founders tried to mitigate.