The FFs believed that the religious persecutions in the name of Christianity, were in fact NOT Christian-like.
You only need look less than 100 years before our independence, in 1692 during the Salem Witch Trials. Hardly the Puritain's shining moment of religious freedoms. Today, Wiccans and the like are allowed to practice whatever they want, BECAUSE by the time 1776 came around, the FFs realized that such persecutions were wrong.
By basing this country on religious freedoms, the FFs were promoting the very basic tennants of Christianity, which is preaching the Gospel, yet allowing people to do what they want religiously.