Classical liberals who were (and are) believing Christians may personally believe that rights come from the Creator, but that does not mean that they believe that religious principles should form the basis of government in a constitutional republic that is religiously tolerant. The whole question revolves around the sphere of morality, in which moral suasion and the freedom of association permit a community to do a great deal to influence the behavior of community members on a voluntary basis. That is different in kind from using the power of the state to enforce a particular Christian denomination's view of morality. If you don't see that difference, you're hopeless.
The fear of theocracy is deep-seated in the classical liberal mind, because classical liberalism developed in the 18th century that was busy trying to liberate itself from really repressive religious regimes, both Catholic and Protestant. Bloody Mary, the St. Bartholomew's massacre, the Revocation of the Edict of Nantes, the English Civil War and the Commonwealth were fresh in the minds of classical liberal thinkers.
Your point about Christianity being under attack to day is true enough, but the attacks are coming primarily from the real left, modern liberals, Marxists and their progeny, not from classical liberals. Classical liberals attitudes towards religion generally reflect the broad tolerance of faiths (or lack of faiths) that has been our tradition in the United States.
The classical liberal's profound distrust of hooking any version of "truth" up to the power of the states is not limited to a fear of theocracy, it is every bit as much directed towards left totalitarianism.
The classical liberal’s profound distrust of hooking any version of “truth” up to the power of the states is not limited to a fear of theocracy, it is every bit as much directed towards left totalitarianism.
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I don’t think this is even close to the historical mark. Where do you get that classical liberals were afraid of anyone that believed in the truth? These were not cultural relativists. The classical liberal was not afraid of people that believed in God. Most viewed religion as a social necessity and most were Christians. The fear was of concentrated power in the state.