America began as a haven for those suffering religious persecution. The founding fathers were aware of that, so they wanted there to be freedom of religion in the Bill of Rights. They were intent on making it possible for Americans to practice their faith, no matter what it was. They further stated that there would be no state-sponsored religion. So, the president or congress cannot suddenly say, "You all must be Baptist or be thrown in jail."
What the founders intended, though, was for religion to thrive in this environment. There is a school of thought that says that religion has no place in public areas - yet this is easily disputed by the following quotes:
-“[July 4th] ought to be commemorated as the day of deliverance by solemn acts of devotion to God Almighty.” John Adams
-“The Law given from Sinai [The Ten Commandments] was a civil and municipal as well as a moral and religious code.”John Quincy Adams
-"It has been the error of the schools to teach astronomy, and all the other sciences, and subjects of natural philosophy, as accomplishments only; whereas they should be taught theologically, or with reference to the Being who is the author of them: for all the principles of science are of divine origin. Man cannot make, or invent, or contrive principles: he can only discover them; and he ought to look through the discovery to the Author.” Thomas Paine
-“Education is useless without the Bible” Noah Webster
“ It is impossible to rightly govern the world without God and Bible.” George Washington
So what does it mean? We do not have to be Christian, Jewish, Muslim - or a believer at all. Yet, we do have to acknowledge that out founders intended for us to have the freedoms we have (speech, press, assembly, etc.) because they were endowed to us by our Creator (as it says in the Declaration of Independence.)
I highly recommend reading The Power and the Glory by Peter Marshall for an in-depth look at this topic.
Hope that helps!