By Daniel Burke, CNN Belief Blog Co-editor

(CNN) - If you don't like it, leave the room.

That's Supreme Court Justice Anthony Kennedy's advice for atheists and others who object to sectarian prayers before government meetings.

In a 5-4 decision written by Kennedy, the Supreme Court allowed Greece, New York, to continue hosting prayers before its monthly town board meetings - even though an atheist and a Jewish citizen complained that the benedictions are almost always explicitly Christian.

Many members of the country's majority faith - that is, Christians - hailed the ruling.

Many members of minority faiths, as well as atheists, responded with palpable anger, saying the Supreme Court has set them apart as second-class citizens.

Groups from the Religious Action Center of Reform Judaism to the Hindu American Foundation decried Monday's decision.

"The court’s decision to bless ‘majority-rules’ prayer is out of step with the changing face of America, which is more secular and less dogmatic,” said Rob Boston, a spokesman for Americans United for Separation of Church and State, which litigated the case.

At least one justice, Elena Kagan, seemed to agree. And while Kennedy's decision reads like a lesson in American history, Kagan's dissent offers a picture of the country's increasingly pluralistic present.

American politicians have prayed before public gatherings since the Founding Fathers crowded into a stuffy Philadelphia room to crank out the Constitution, Kennedy writes.

The inaugural and "emphatically Christian" prayer at the First Continental Congress was delivered by an Anglican minister, who overcame objections from the assembled Quakers, Anabaptists and Presbyterians.

The prayer united the mostly Christian Founding Fathers, and the rest is history, Kennedy writes.

So, the justice suggests, as long prayers at public meetings don't fall into a pattern of proselytizing, denigrating nonbelievers or threatening damnation, what's the problem?

According to a recent poll, the vast majority of Americans share Kennedy's view.

Less than 23% of Americans told pollsters at Fairleigh Dickinson University that they dislike prayers at public government meetings.

“This has always been a praying nation, despite its very secular Constitution,” said Peter J. Woolley, professor of comparative politics at Fairleigh Dickinson in Hackensack, New Jersey.

“People generally see generic prayer as harmless, if not uplifting, not as something that is oppressive.”

But what about people who like their local government meetings to be religion-free?

"Should nonbelievers choose to exit the room during a prayer they find distasteful, their absence will not stand out as disrespectful or even noteworthy," Kennedy writes.

Kagan, writing for the dissenting minority, sharply disagreed.

She suggested that the five justices who formed the majority - all of whom are Catholic - don't understand what it's like to belong to a minority faith in America.

The Supreme Court's Catholic majority seems to think that, because many prayers before government meetings take on a ceremonial aspect, the actual content of the prayers doesn't matter, Kagan continues.

In essence, she said, the majority is making light of religious differences while conferring a special role on Christianity.

"Contrary to the majority's apparent view, such sectarian prayers are not 'part of our expressive idiom' or 'part of our heritage and tradition,' assuming that 'our' refers to all Americans. They express beliefs that are fundamental to some, foreign to others - and because of that they carry the ever-present potential to divide and exclude."

To illustrate her point, Kagan, who is Jewish, raises a hypothetical scenario.

Let's say there's a Muslim resident of Greece, New York, who appears before the town board to share her policy views or request a permit.

Just before the Muslim woman makes her argument, a minister "deputized by the town" asks the room to pray in the name of "God's only son Jesus Christ."

With less than a dozen people the room, every action is noticed.

So, the Muslim woman has two choices, Kagan argues: 1) Go along with the majority and pray, despite her religious objections, or 2) Risk causing some kind of disturbance or public disagreement with the very people she is trying to persuade.

"And thus she stands at a remove, based solely on religion, from her fellow citizens and her elected representatives," Kagan writes.

Kagan did not suggest that the Supreme Court's majority (Kennedy, Chief Justice John Roberts and Justices Antonin Scalia, Clarence Thomas and Samuel Alito) voted to uphold sectarian prayer because they are members of the country's largest church, Roman Catholicism.

But Ronald Lindsay of the Center for Inquiry, a Humanist group, called it "striking and sad" that "five of the six Christian justices on the Supreme Court formed the majority." (Justice Sonia Sotomayor, who is Catholic, voted with Kagan.)

"With a Supreme Court that appears hostile to the rights of religious minorities, those of us who believe in a secular government must redouble our legal and advocacy efforts,” Lindsay said.

Of course, there's a great gap between being Catholic and using the gavel to promote Christianity.

But a new study conducted by scholars at the University of Southern California offers intriguing insights into how the justices have voted on First Amendment issues.

The upshot: The conservative justices tend to side with conservative causes; the liberals with liberal ones.

"Supreme Court Justices are opportunistic supporters of the First Amendment," write the scholars.