Not only does the 14th Amendment apply the Fedeal Bill of Rights to the states, but the Constitution also says the Federal Government must guarantee "a republican form of government" to the states. The states could not simple trample the religious rights of individuals just because they aren't "congress".
It would also be silly to presume that the Founders would go to all the trouble of ratifying the Bill of Rights that restricts only the Federal Government, but allows the state of California to force me to convert to Buddhism, take my guns away, place the National Guard in my house without my consent, and suspend my right to habeas corpus. OF COURSE THE BILL OF RIGHTS EXTENDS TO STATES!
Actually, that wasn't the case, as Virginia had a state church until the year before. See:
http://www.thediocese.net/Diocese/whoweare.htmThe ist Amendment, in theory, didn't prohibit states from entering into the religious realms. The 14th does, but went it was adopted, no state would have thought of doing it.