Separation or Coexistence?

As the number of presidential candidates dwindles, those who would attempt to influence our vote are already pointing out religious differences between the remaining choices. I can see it coming - we'll end up focusing way too much on "faith" and ignore important platform issues like foreign policy and health care. After all, remember the 11th-hour subcampaign in 2000 where prominent Christians put on the full-court press? Such a campaign against either of the current Democratic frontrunners could have even more impact (after all, they've already attacked each others' faith!).
So, before it happens, let's discuss how important religious differences between the candidates should or should not be. To begin, I have a problem with the anonymous characterization that the Supreme Law of Our Land provides for the "separation of church and state." In fact, the provision states that "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof." Free exercise by those who govern as well as by those who are governed. Sounds more like "coexistence" than "separation." Second, as diverse as our nation is, shouldn't I expect the possibility that the one individual most qualified to hold the office of president has different religious views than I have?