The first part of your post can be summed up by saying, that state establishment of a church creates a potential for abuse of individual liberties. But surely you can see that the 14th amendment only prohibits actual violations of liberties, that is, actual limitations on people's autonomy. As for your other point:
Now, you could, I suppose, point out that you are already forced to support secular ideas you disagree with through compulsory taxation. But religion is supposed to be treated differently in the first place, not as basely as more worldly political ideas and theories.
That it's "supposed to be treated differently" does not establish that not treating it differently in any way limits our autonomy as individuals, which is what the 14th amendment proscribes.
Would that it were so - the courts can and do entertain facial challenges to laws and state actions all the time. Suppose your state were to make castration the penalty for jaywalking - must we wait until someone is actually facing that sentence before we act, or should not the courts be able to determine that such a law is invalid on its face, under the Eighth Amendment? Or maybe you don't think it's "cruel and unusual"? ;)
That it's "supposed to be treated differently" does not establish that not treating it differently in any way limits our autonomy as individuals, which is what the 14th amendment proscribes.
You may be right, but given the state of First Amendment law, this is still ultimately a normative argument. Whether or not it should be treated differently, it is treated differently, and not without some historical and legal justification, either.