Because Virginia did not wish to have a state religion and have in place the coercive power of the state in favor of one specific religion. This would offend the freedoms of conscience and belief. A read of the debates on this provides further clarification. It was never meant to refute the Biblical basis of the founding principles.
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"in proof that they meant to comprehend, within the mantle of its protection, the Jew and the Gentile, the Christian and Mohammedan, the Hindoo and Infidel of every denomination."