The Constitution of the United States protects freedom of religion overall, to include freedom from religion. A single word, a subtle but extremely important difference.
The constitution has an inherent Christian bias built into it. That it would be so was not remarkable to the men who created it. Their stipulations about no religious test for office had less to do with tolerance of other religions than it did for tolerance of other Christian Denominations.
In 1787, some states had their own official state religion, and knowing what they did of the religious wars in Europe, the founders wisely realized that emphasizing one denomination over another was a sure fire way to blow apart the Union, but by making it absolutely clear that no one would be excluded on the basis of whatever version of Christianity was popular in their state, they secured the consent for the new government from the citizens of those states who saw this as a reasonable compromise.
Probably Jefferson (not a member of the convention) was the only one who contemplated tolerating Muslims in this whole concept.
In the context of the Period, the founders used the word "Religion" as we would nowadays use the word "Denomination." That the nation would be vastly dominated by various forms of Christianity was to them, an assumed given.
It has always been so until comparatively recently. (last 60 years.)