The Rachel Maddow Show blog has the article Divided Court backs town-meeting prayers.
Justice Anthony M. Kennedy, writing for the majority in the 5-to-4 decision, said “ceremonial prayer is but a recognition that, since this nation was founded and until the present day, many Americans deem that their own existence must be understood by precepts far beyond that authority of government to alter or define.”
In dissent, Justice Elena Kagan said the town’s practices could not be reconciled “with the First Amendment’s promise that every citizen, irrespective of her religion, owns an equal share of her government.”
By what definition is recognizing one religion over another or over no religion not an establishment of religion. It establishes that one religion is favored by the government entity over another.
I did find a reference in synonyms for recognized to the word establish. So Justice Kennedy’s words could be edited for style to be “ceremonial prayer is but an establishment that, since this nation was founded and until the present day, many Americans deem that their own existence must be understood by precepts far beyond that authority of government to alter or define.”
It is also easy to dismiss the significance of a particular prayer when that prayer is from your own religion. How does it make the people not of that religion feel?