The first amendment states "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances." The basis of the separation of church and state, that Thomas Jefferson wrote to Danbury Baptists, are in line with "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof". If you was to read the letter, which is really the only backing to separation of church and state, you would see that it says nothing about keeping religion outside of the government.