Jefferson was writing about the Bill of Rights, and the "Wall of Separation" was in reference to the 10th amendment, and how there should be a wall of separation between the Federal Government and the States. This has always been strictly in the context of States Rights. It never had anything to do with Churches at all. Oh, excuse me, the Danbury Baptists asked the question that Jefferson was answering. In that case, yes, it had to do with churches. Other than that, he merely replied that the 2nd Amendment applied to the Federal Government and not the States, because the 10th Amendment put a "wall of separation" between the Federal Government and the State Governments.