Although Trump could be "marginally better" than Clinton on religious freedom in that he would hire staff members who did not promote radical secularism, "I don't really see Mr. Trump mounting much of a challenge to the agenda of the sexual revolution on same-sex marriage and transgender issues," Franck said.
"On a generous reading of his statements, one might imagine that Trump simply doesn't care about religious freedom, and perhaps doesn't understand what is at stake," Rachel Lu, a professor of philosophy at the University of St. Thomas, wrote for the Religious Freedom Institute.
For instance, Trump "waffled on North Carolina's transgendered bathroom law, but his immediate impulse was to criticize the state for infringing on the rights of the transgendered," she wrote.
Trump was asked about religious freedom by EWTN's Raymond Arroyo on "The World Over" last Thursday.
He responded by championing the repeal of the Johnson Amendment, which prohibits clergy from endorsing political candidates from the pulpit, and as Trump put it, stops faith leaders from endorsing him as a candidate.
"I think it's one of the most important things that I'll be doing for the evangelicals and for religion," he said. "So, I think it's very, very important."
However, while repealing the amendment is a good step, it is "way, way down the list [of importance] for every religious leader I talked to," Franck said.
Furthermore, some say Trump's rhetoric toward ethnic and religious minorities has inflamed social tensions and could spell trouble for them if he is elected president.
In a piece published by the Religious Freedom Institute, two representatives of the Ahmadyyia Muslim community harshly criticized Trump for his rhetoric and policy proposals for religious minorities, saying the policies are a "sharp departure from anything that we have seen in decades."
In addition to his proposed Muslim ban, Trump had advocated the "surveillance of certain mosques" as a national security measure in the wake of the Paris attacks.
"It has become apparent that Trump responds emotionally to current events and does not always think his proposals through and whether or not they violate the principles of the constitution," Rasheed Reno and Qasim Rashid wrote. "They are often inspired by fear and anger which is a dangerous and irresponsible use of a leadership position."
This volatile behavior by a presidential candidate could spell danger for religious minorities under his administration, they insisted.
"When a president shows willingness to violate the civil liberties of its citizens," like through a Muslim ban, "it sets a dangerous example which leads to violence and unrest against religious minorities," they added.
"This has already been demonstrated in the short period of Trump's candidacy, where violence against Muslims and other minorities has increased significantly."
When he was asked by a Muslim-American about this uptick in violence during the second presidential debate, instead of explaining how he would protect the religious freedom of U.S. Muslims, Trump immediately pivoted to the need for Muslims to report suspicious activity in their own communities, they pointed out.
What can Catholics do when religious freedom is under attack, and may continue to be under attack in the next presidential administration? Church leaders must continue publicly defending it, Lewis maintained, pointing to initiatives like the U.S. bishops' Fortnight for Freedom campaign.
Also, though the eyes of the nation are on the presidential race, there are plenty of key congressional races, Lewis added. "We have to know what the views of candidates for Congress are on these questions as well," he said, as "it's in their hands to approve legislation" like the First Amendment Defense Act, which would establish religious freedom protections.
The Church must also tell its story if religious charities are to gain a sympathetic ear from the public, he said, as the freedom of religious charities is threatened by laws like the birth control mandate and state laws preventing churches from serving undocumented immigrants.
"It's important to continue to articulate the fact that those institutions do their work as part of their apostolic commissions," Lewis said. "It's not the case that the Church just runs charitable organizations just to run charitable organizations."
"There's no separating what they do from the very heart of the Christian mission."