It is confusing. I am not sure I got it right but will try. The Court held in 1989 that the “separation of church and state” does not mean that branches of the government need be totally atheistic. They are free to hold prayers before meetings, to display religious symbols etc as long as they do not coerce anyone to participate in the religious activity. The court was saying that the First Amendment means you will be offended from time to time.
In the more recent decision, it appears that a school had been holding graduation ceremonies in a church. Someone sued saying this was inappropriate and the courts agreed. The Supreme Court did not take up the case, which basically means that the Court is moving away from its 1989 decision. Scalia was saying “hey, as long as you are not forced to pray, holding the event in the church is not big deal” but the court refused to hear the case, signalling that the court thinks this is crossing the line to coercion.
Maybe this is the worst ever written article. Ever.