The conventional wisdom surrounding American college life these days views campuses as hotbeds of intolerance for free speech, with students themselves leading the charge.

But a new report by PEN America, to be released on Monday, questions that story line while warning of a different danger: a growing perception among young people that cries of “free speech” are too often used as a cudgel against them.

The report, titled “And Campus for All: Diversity, Inclusion and Freedom of Speech at U.S. Universities,” covers a broad range of hot-button topics, including trigger warnings, microaggressions, safe spaces and controversial campus speakers. While it cites “troubling incidents of speech curtailed,” it finds no “pervasive” crisis.

But it does worry about an “apparent chasm” between free speech advocates and student activists, thanks in part to a conversation that sometimes dismisses students’ demands for equity and inclusion instead of parsing how they do, or don’t, infringe on the “bedrock principles” of free speech.

“A rising generation may be turning against free speech,” the report warns. “Before these developments deepen and harden, PEN America hopes to open up a wider, more searching dialogue that can help all sides to these debates better identify common ground.”

Campus speech debates are somewhat new territory for PEN, a writers’ organization that historically has been concerned with protecting authors and journalists around the world, whether from censorship and imprisonment or more amorphous threats like electronic surveillance.

But Suzanne Nossel, the group’s executive director, said the report was consistent with PEN’s broad mission, which includes promoting more diverse voices through projects like its annual World Voices Festival of International Literature.

It is also, she said, a departure from the “doctrinaire ‘free speech or bust’ position.”

“There’s a lot of attention in the world of free speech advocacy to barriers to expression,” Ms. Nossel said. “There has been somewhat less given to what needs to be in place to enable and unleash expression.”

The report arrives at a moment when many free-speech advocates see a growing, and troubling, generational divide. A Gallup poll last spring showed that college students were overwhelming in favor of free expression on campus in general but also significantly in favor of some restrictions on “intentionally offensive” speech.

“From an old-fashioned free-speech perspective, it strikes one as contradictory,” said Alberto Ibargüen, the chief executive of the John S. and James L. Knight Foundation, a sponsor of the poll.

The PEN report digs right into those seeming contradictions. It outlines the cases for and against demands for safe spaces, trigger warnings (which some students demand be given with class assignments relating to difficult topics, like sexual assault) and campaigns against so-called microaggressions (small, often unintentional racial or other slights), and then explores the ways they do, or don’t, conflict with free expression.

Jerry Kang, the vice chancellor for equity, diversity and inclusion at the University of California, Los Angeles, said he appreciated PEN’s efforts to understand students’ point of view.

“It’s very smart and thoughtful and avoids caricature,” Mr. Kang, a legal scholar who has studied implicit bias and was interviewed for the report, said. “They are fully committed to robust, uninhibited speech. But they also recognize that words matter.”

But some prominent free-speech advocates who have seen the report had a more mixed reaction.

“In terms of raising the issues and presenting the on-the-ground facts in a serious and fair-minded way, I think it’s a big step forward,” said Floyd Abrams, the First Amendment lawyer. “But I find it hard to read its extraordinarily powerful depiction of things that have happened on campus without concluding there is a crisis of great magnitude.”

The report’s three main case studies cover complex conflicts on three campuses that drew intense media coverage in the past year: over the line between criticism of Israel and anti-Semitism at U.C.L.A.; over sexual harassment, academic freedom and Title IX protections at Northwestern University; and over free speech and Halloween costumes at Yale University.

PEN finds significant threats to free expression in some of those cases. At Northwestern, the report cites both the difficulties of redress for victims of alleged sexual assaults, and the way the vagueness of Title IX, the federal law that prohibits sex discrimination in education, can “chill speech” and “encumber academic freedom.” (The report calls on the federal Department of Education to clarify that a subjective sense of offense is not enough to prove there is a hostile environment.)

But at Yale, the report suggests, the students who protested against an administrator who sent a now-famous email questioning prohibitions on offensive Halloween costumes were not attacking free speech rights, but exercising their own.

That depiction cuts against the pervasive narrative, as well as the position of the most prominent voice on campus speech issues, the Foundation for Individual Rights in Education, or FIRE, which has strongly defended the administrator who sent the email, Erika Christakis. (Ms. Christakis eventually resigned from both her administrative and teaching positions.)

Greg Lukianoff, the president and chief executive of FIRE, said that he welcomed PEN’s report, some of which was described to him by a reporter.

But he questioned both the thrust of its account of the Yale incident, as well as the perception among many progressive students and faculty that the campaigns to protect free speech rights have been put in service of a right-wing agenda.

“Right now, it’s true, some of the louder voices are libertarian or conservative,” Mr. Lukianoff said. “But free speech is something we should all be able to come together on.”

The PEN report may be broadly sympathetic to students, but some of them may be hard to win over. While it supports limited, voluntary “safe spaces” within campuses where students can “recharge” with those from a particular group, it calls for campuses as a whole to be seen instead as “safe places” — free of physical danger, but “intellectually and ideologically open.”

Storm Ervin, a co-founder of Concerned Student 1950, a group at the University of Missouri that organized protests last fall against what many students saw as a racially hostile environment, said that she recognizes the importance of free speech.

“Free speech is the reason we were allowed to protest,” she said in an interview.

But Ms. Ervin, like many fellow students, does not see untrammeled free expression as always the paramount value, or one that is easily reconciled with equality and inclusion.

“I understand what is meant by ‘the campus as a whole is better conceived as a safe place,’” she said in a subsequent email, citing a passage in the report. “But I think we, the author and I, can agree that that campus is not a psychological safe space for all, and part of the reason is that of free speech.”