People protest the travel ban outside  the Supreme Court on Tuesday. Many legal and advocacy groups that focus on religious liberty were silent on the ruling Tuesday. (Mandel Ngan/AFP/Getty Images)

Three weeks ago, many religious-liberty advocates celebrated the Supreme Court’s decision that a Colorado baker should not have to create a gay wedding cake, saying the baker’s religious faith was disparaged by the government and that could not stand. But some of the same groups met with silence the court’s decision Tuesday to uphold what President Trump reportedly called his “Muslim ban.”  The difference in response raises new questions about what precisely is meant by religious liberty in America today, lawyers who focus on the area say.

Compared with other recent federal rulings about religious liberty, “I would have said we were in a period when the court was caring more about religion,” said Noah Feldman, a constitutional law scholar at Harvard University who focuses on law and religion. “But this makes it look like what the court cares about is the religion of evangelical Christians, not Muslims. It makes it look like the Supreme Court doesn’t have a general concern for religion. It looks badly motivated.”

In the decision Tuesday, the Supreme Court majority cited comments from Trump as a candidate and as president, such as “Islam hates us,” and his call for a “total and complete shutdown of Muslims entering the United States.”

But the five justices wrote in their opinion that “the issue before us is not whether to denounce the statements. It is instead the significance of those statements in reviewing a Presidential directive, neutral on its face, addressing a matter within the core of executive responsibility. In doing so, we must consider not only the statements of a particular President, but also the authority of the Presidency itself.”

Many prominent legal and advocacy groups who describe themselves as focused on religious liberty put out no statements Tuesday about the travel-ban ruling, despite the arguments raised in the case about religious discrimination. In contrast, the groups, which were primarily of the conservative bent,  put out immediate statements Tuesday about another decision by the court — one saying antiabortion crisis-pregnancy centers cannot be required to tell clients about the availability of other state-offered services, including abortion.

The exception was the U.S. Conference of Catholic Bishops, which put out a statement Tuesday praising the pregnancy center decision and then Wednesday released one quoting the two bishops who chair its committees on migration and religious liberty:

“The travel ban targets Muslims for exclusion, which goes against our country’s core principle of neutrality when it comes to people of faith. We are disappointed in the Court’s ruling because it failed to take into account the clear and unlawful targeting of a specific religious group by the government,” said the statement by Bishop Joe S. Vásquez of Austin and Archbishop Joseph E. Kurtz of Louisville.

The religious liberty groups that did not initiate any statements on the travel ban ruling included Becket; the Ethics and Religious Liberty Commission, which is the policy arm of the Southern Baptist Convention; and the Alliance Defending Freedom.

Several more liberal religious-liberty groups spoke out against the ruling as discriminatory, including the Interfaith Alliance and the Baptist Joint Committee on Religious Liberty.

Conservative-leaning groups that did offer comment Tuesday, when asked by the Post, said that they didn’t consider the travel-ban case to include a key religious-liberty value, and instead viewed it through a national-security lens.

Bruce Hausknecht, a lawyer at Focus on the Family, said his organization would take no side on the ruling.

“In the first instance, it’s about national security. That’s not a Focus on the Family issue,” he said.

“The travel ban gets into a lot of political [issues], more than our focus on religious freedom,” said Rick Henshaw, spokesman for the Catholic League for Religious and Civil Rights.

Elizabeth Bristow, press secretary for the Southern Baptist policy group, Tuesday noted in response to a request from the Post that the group’s leader, Russell Moore, put out a criticism of Trump’s initial executive order on the ban, in January 2017. Moore’s carefully worded letter then never specifically called out discrimination against Muslims, and was a general call to protect refugees and also not to rock the boat in Muslim-majority nations where Christians volunteer or work.

Moore, who represents a group that is largely made up of political conservatives, wrote in the 2017 letter that the White House must “affirm your administration’s commitment to religious freedom and the inalienable human dignity of persecuted people whether Christian, Jewish, Muslim, Yazidi or other, and adjust the Executive Order as necessary.”

On Tuesday, Bristow said the group didn’t put out a statement on the Supreme Court ruling because debate on the current version of the ban was “more specific to national security questions rather than particular religious communities,” she wrote in an e-mail, so “it placed the issue outside of those we normally address.”

The Faith & Freedom Coalition, run by Christian Coalition founder Ralph Reed, put out a statement praising the Supreme Court ruling. The group, its statement said, supports the White House policy of cracking down on countries “plagued by civil war, terrorism and radical Islamic extremism that pose a danger to our national security.”

Becket responded to the Post’s question about its silence by noting the brief it filed in the case, which was neutral on the allegation of discrimination and took no side as to whether Muslims were targeted. Becket’s brief focused on its criticism of the legal strategy of those challenging the travel ban.

But some constitutional lawyers, including Feldman,  found the decision and the groups’ silence worrisome for religious freedom.

Jed Shugerman, a law professor at Fordham University, said he agreed with the June 3 decision about the Colorado baker, saying it was written in a neutral way to push back against the apparent anti-religious bias shown against the Christian baker by the state commission which penalized him. The commission compared the conduct of the baker, who agreed to sell the couple a cake, but not a wedding cake, to slavery and the Holocaust.

“It’s now today hard to look back at [the June 3 ruling] as a principled compromise,” Shugerman said.

“The big picture is, if you take a step back, it’s troubling that when it comes to religious liberty, there are certain religions that get a lot of protection for conscience, for their members, their freedoms,” he said, noting the 2014 Supreme Court decision known as Hobby Lobby, which found that corporations can’t be forced to violate their own religious beliefs. In that case, the owners of the craft-store chain were opposed to providing for employees certain kinds of birth control.

“But bias against Muslims just coincidentally doesn’t get a judicial notice,” Shugarman said. “We have to start asking questions about whether this court is committed to religious liberty or to Christian liberty?”

The Post asked Kristen Waggoner, vice president of Alliance Defending Freedom, on a conference call Tuesday about the travel ban Trump described as aimed at Muslims. The call was organized to praise the ruling about crisis-pregnancy centers.

“I don’t think the two are related in terms of that,” Waggoner said. She hadn’t yet read the travel-ban ruling, she said.

Julie Zauzmer contributed to this report.

This story has been updated.