It took an obscure order issued on the last day of the recent term for Justice Samuel Alito to drive home the point. By refusing to consider a family-owned pharmacy's objection to a Washington state regulation forcing it to stock and sell emergency contraceptives, he warned, the court was sending an "ominous sign."

"If this is a sign of how religious liberty claims will be treated in the years ahead, those who value religious freedom have cause for great concern." Alito said.

Indeed, to some groups that work at the intersection of law and religion, the court appears to be taking a left turn on issues where it has steered right in the past -- a trend that, if it continues, could affect an upcoming case involving a Missouri church's effort to qualify for state playground funds and potentially another challenge to the pharmacy rule.

Under Chief Justices William Rehnquist and John Roberts, the court generally has carved out protections for religious groups and individuals. In recent years, it ruled that a Missouri church could sidestep employment discrimination laws, private corporations could avoid federal health regulations regarding contraceptives, and a New York town could open meetings with Christian prayers.

Last year, it ruled in favor of a Muslim prisoner who sought to wear a beard, a Muslim woman denied a job because she wore a headscarf, and a tiny Arizona church that protested municipal restrictions on street signs.

But after ruling for the craft giant Hobby Lobby in the 2014 contraceptives case, the court did not side with religious non-profits or the government this year in similar cases, instead sending them back for further appellate review. It struck down Texas restrictions on abortion clinics and, on the final day of the term, refused to hear the pharmacy's petition.

Seeing 'red flags'

That case was brought by the Stormans family, which operates Ralph's Thriftway in Olympia, Wash. The family had what conservatives considered a slam-dunk case against a unusual state regulation that pharmacies must fill prescriptions for contraceptives, including morning-after pills that prevent a fertilized egg from reaching the uterus.

"Ralph's has made a strong case ... that the regulations here are improperly designed to stamp out religious objectors," Alito wrote in his dissent, joined by Roberts and Justice Clarence Thomas. In his final footnote, Alito invited another legal challenge.

​Kristen Waggoner, who represented the pharmacy through a federal district court victory and an appeals court defeat, says it's too soon to assume the court has shifted on religious freedom cases. But she says the refusal to hear the Stormans case "does cause you to wonder."

"We're seeing the red flags," Waggoner says. "The risk is Americans will no longer have the right to live consistent with their faith without punishment from the government."

Some defenders of religious freedom don't share Alito's fear for the future.

"The court has been responsive to religious liberty claims in most of the cases in recent years," Eric Rassbach, deputy general counsel at the Becket Fund for Religious Liberty, says. "I don't see a reason to think that the court is going to become deaf to religious claims."

Douglas Laycock, a religious liberty expert at the University of Virginia School of Law, says the risk arises when core issues important to liberals are at stake, such as women's access to all methods of birth control.

"The liberal justices are willing to protect religious liberty when their more favored issues are not at stake, or perhaps when the case is clear enough," Laycock says.

Advancing equality

But when other interests such as preventing discrimination against women, gays and lesbians, or minorities are involved, the court's latest responses please liberal groups.

"Religious liberty doesn't give you a right to impose your views on others," Louise Melling, deputy legal director at the American Civil Liberties Union, says. She sees the court's recent actions as "part of a broader move to advance equality."

Many conservatives are wary that the court -- stripped of Scalia's influence and vote, and often controlled by the more mercurial Justice Anthony Kennedy -- increasingly may favor government regulators over religious believers.

"What we're seeing is a sort of shift around social norms" concerning sexuality, says Jay Richards, assistant research professor at The Catholic University of America in Washington, D.C. "Kennedy is the best Geiger counter. He's a very good instrument for measuring that."

The next test will come in the fall, when the justices consider a Missouri church's challenge to being denied state funds for playground resurfacing. A second case involving the pharmacy regulations also could be headed their way in the future, along with lawsuits from merchants who refuse to participate in same-sex weddings.

"There's more and more of these cases coming up," Waggoner says. "This is not over."