Jerry Seinfeld knows his way around handling awkward moments onstage. Even so, the initial reception he faced at Duke University’s commencement on Sunday reflected a more complicated audience than usual.

As Mr. Seinfeld, who has recently been vocal about his support for Israel, received an honorary degree, dozens of students walked out and chanted, “Free, free Palestine,” while the comedian looked on and smiled tensely.

Many in the crowd jeered the protesters. Minutes later, as the last…