Speculations on Church and State

The United States of America prides itself in it's separation between church and state. The first amendment of the constitution says "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof" (U.S. Constitution). This is a strong statement and one that has been found difficult to follow due to the fact that many key moral issues are often intertwined with religions of various sorts. In his speech regarding his religion as it related to presidency, John F. Kennedy proclaimed that he thought religion should not matter in terms of state.

Here is the clip.



However, it has been more difficult to separate the two than many Americans realize. There are many different ways that religion has leaked into public matters. Consider the pledge of allegiance "one nation under god" or the publicly funded boy scouts of America (a christian organization). Religion also shows up on money, remember the "IN GOD WE TRUST" on coins?
Perhaps the most obvious evidence of the encroachment of religion on American rights and everyday life is that of the Gay marriage issue. Homosexuals are not permitted to become married in most of the states. The prevention of same-sex marriages is largely based on the religious belief that marriage is between a man and a woman. My point is not to take sides regarding this issue but instead to acknowledge that it is a huge example of how America has yet to fully separate it's politics from it's religion(s). As another example, people who are not "of God" are not allowed to take political positions of power in many states including Massachusetts and Texas. While this does not discriminate against any religion in particular it certainly respects the establishment of a religion (even though this is against the constitution) and keeps atheists from being in office.
This difficulty in keeping church from state is due to the fact that many morals are based on some sort of religion. While there are many atheists and they also have morals, they are in the minority in America, therefore these many issues such as gay marriage, are being decided with religious bias.
Will it ever be possible to separate Church and state while the religious are in the majority? The lesser aspects such as the God references in the pledge of allegiance and on coins have more potential to be changeable (since they are not as rooted in morals). However, the more important issues are still governed by what people believe, and, since we as a democracy go by majority rules, is it possible to assume that we will not be able to fully separate Church and state until there are more atheists than religious people in America?