Public education even in 1850 is nothing like public education today.
Also, you ignore the debates about the First Amendment itself in Congress. If you read the Annuals of Congress records, it is clear the establishment clause was never intended to go as far as it did today.
I would say it does go slightly further than what some claim, that it only banned a state church. But, it was never intended to go as far as the SCOTUS interprets it today.
It should be noted that for all the talk of that law, Virginia was not exactly following pure separation of church and state even after its adoption.
The difference between an acorn and an oak tree. To tax someone for a purpose other than protecting an inalienable right is robbery.