The wall Jefferson referred to is designed to divide church from state, not religion from politics. Church and state are specific things: the former signifies institutions for believers to congregate and worship in the private sphere, the latter the collective milieu of civic and political and legal arrangements in which we live while in the public sphere.
The church is private religion—be it evangelical or mainline Protestantism, conservative or liberal Catholicism, Orthodox, Reform, or Conservative Judaism, or any variant of Islam, Buddhism, Hinduism, and so on.
The specific beliefs, practices, and positions of any faith are protected from government interference by the First Amendment, which mandates religious freedom. Yet the Founders consciously allowed a form of what Benjamin Franklin called “public religion” to take root and flower at the same time they were creating a republic that valued private religious liberty.