How does that relate to discrimination?
In the court case you link, while im not going to read the...20 page? ruling from scotus, it appears they are talking about an area of Maine where there are no other schools available? And, publicly available tuition money was being withheld solely on basis of the schools religious nature. They are suggesting that it violate the free exercise clause to specifically exclude a school based on its religious charter.
Also, from my understanding, the establishment clause is a barrier from the federal government establishing a national religion, which this court ruling doesn't do. This is a case of a states use of publicly available tuition money. The establishment clause applies to the federal governments interaction with religion. I mean, does the state give money to any other private organization? If so, how could you disparage one group just because they are religious by nature.
It appears that the state constitution mandates that every child gets a free public education, but some parts of the state are very remote, so they allow the parents to choose a school and that school could be public or private. As long as the school is accredited, they are eligible for the tuition payments. Some of these schools may be religious by nature. The state, nor the federal government are not establishing a religion in doing this, right?