The Constitution does not speak to the separation of church and state. What it does is prohibits Congress from passing laws establishing a state religion. It doesn't mean Congress cannot treat religious institutions as viable contributors to our society.
Also, the Constitution does almost nothing to restrict state level action. I don't know who the devils were who first began applying the whole thing to the states, but it was a devious move to subject the states to Federal rule, when it was supposed to be the opposite.
https://www.theguardian.com/us-news/2025/apr/30/supreme-court-charter-schools