Jonathan Chait has a great post noting that in the early 19th century it was illegal to build synagogues in many states. He compares this to the Cordoba House controversy. Excellent point. He does express surprise about something which is not at all surprising writing
"even after the signing of the Constitution, First Amendment protections didn't stop cities from preventing the construction of Jewish housesof worship"
I will pass over the fact that, when it was signed, the Constitution was just the skins of 3 dead sheep. It only became a constitution when it was ratified. Then the bill of rights was a twinkle in Samuel Adam's eye. The bill of rights only saw the light of day two years after the signing of the Constitution.
A more important point is that the first amendment in no way guaranteed freedom of religion. It only prevented "congress" from restricting freedom of religion. Only state constitutions offered any protection of freedom of religion from state legislatures. The first amendment begins "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;..." so it restriced congress only and left state legislatures to ban synagogues, mosques or churches as they saw fit.
The US Constitution only established freedom of religion (all by itself without help from state constitutions) when the 14th amendment was ratifies. The key claus
"All persons born or naturalized in the United States, and subject to the jurisdiction thereof, are citizens of the United States and of the State wherein they reside. No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any State deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws."
Notice that the "priviledges and immunities" are those of citizens. As far as I can tell (which isn't far) repeal of the first sentence (as proposed by Sen Graham) would make it possible to, say, declare that Jews aren't citizens and don't have the priviledge of building houses of worship. It seems to me that a state law which offered jews and gentiles equal protection from synagogues would be consistent with the text as re-written.
I never cease to be amazed at how often web-literate people write about the constitution without checking the text which is easily available.