The separation of Church and State is not meant to hinder religion, or to deny the role of religion in society or in our history. Many of the founders were Christians, even James Madison was a Christian, but what they established was a government that was non-religious - a secular government. That does not mean that they rejected religion; their purpose was to establish a government whose sole function was to administer earthy matters, while matters of religion were left purely to ecclesiastical institutions. The founders, by and large, were very much supportive of the role of religion in society, but they separated the ideas of society and government, leaving religion to play a role in society, not government.

If you believe strongly in your religious beliefs, you should fear that someone will try to impose his own beliefs upon you.  On a similar note, what you believe today may not be what you believe tomorrow, so why solidify your beliefs of today forever?