We’re not just talking about laws enacted by Congress:
“In 1947 the Supreme Court held in Everson v. Board of Education that the establishment clause is one of the liberties protected by the due-process clause. From that point on, all government action, whether at the federal, state, or local level, must abide by the restrictions of the establishment clause.”
source: http://www.firstamendmentcenter.org/rel_liberty/establishment/index.aspx
And nobody here is talking about creating law by popular vote, so I don’t know why you brought that up.