An those Many, Many Courts are in fact WRONG. The founding fathers of this country all supported the use of public moneys in religious functions that benefited the public. The establishment clause, as you put it is a creation of the courts, not of the constitution. You your self quoted the 1899 decision by a Court, not basing any of it on the words of the constitution. Show me the word "separation" in the constitution, it is not there, therefor it in not valid to use in a discussion of the meaning of the constitution.
As for the Judiciary understanding what the founding fathers meant, that may have been true 150 years ago, but it is not true now. The words of the constitution mean something, when they were written, how they were used. Hence the recent 2nd amendment case.. "the right of the people... shall not be infringed." Judges have been deliberately misapplying that amendment to allow the unconstitutional restriction of ownership of arms. There decision were based on politics not on the words of the constitution, the times in which it was written, the usages of the language, and the intent of the writers of the constitution.
Read the Federalist papers, the Writings of Adams, Madison, Monroe, you will find out the courts have bastardized the meaning of the constitution since at least the creation of the reconstruction amendments. Example, "separate but equal" is not in the constitution but was decided by the Courts and being Constitutional. That was wrong, the decision was made by a court more worried about politics in the south than the words and the meaning of the amendment.
If separate but equal is unconstitutional because it is not in the constitution, then the concept of separation of church and state is not valid as it is not in the constitution.
You, unfortunately, have been brainwashed and really do need to study the constitution, its writing, its history. Court decision do not follow the constitutions meaning all the time.