This decision basically changes nothing. It just stops a state from discriminating against religions.
If you are getting hung up on the words "separation of Church and State," please note that those words are not in the Constitution. That phrase (a version of which was penned by Jefferson in private correspondence) is just used to summarize the First Amendment's religion provisions, which are actually as follows:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof....
Separation means the State cannot show favoritism for, or discriminate against, religion. In this case, it was showing discriminating against religion by providing a benefit only to secular school students and denying that benefit to religious school students.
And, where would you go, by the way? Many countries have no seperation of church and state.