Taken completely on its own, I would argue that article 11 does, in fact, establish that the United States is not a Christian government. However, and any respectable academic would agree, you cannot simply look at one piece of evidence to try and establish a historical (or any other) fact. In history, you must look at evidence that is contradictory in order to gain a more precise understanding of context. Take, for example, this
1798 proclamation from President John Adams, who was president when the Treaty of Tripoli was ratified, which states,
“[T]he safety and prosperity of nations ultimately and essentially depend on the protection and the blessing of Almighty God, and the national acknowledgment of this truth is not only an indispensable duty which the people owe to Him, but a duty whose natural influence is favorable to the promotion of that morality and piety without which social happiness can not [sic] exist nor the blessings of a free government be enjoyed.”