The problem with what Franklin Graham is saying is obvious because he presumably knows that moderate Muslim Duke University students have nothing to do with any attacks against Christians. If it is true that rogue factions of a faith who act unjustly and terrorize others prohibits that entire faith from freely using Duke's chapel to pray, then Christians should've been prohibited from using it from 1900-1970 as so-called Christian members of the KKK terrorized African Americans all over the American South.
Truthfully, though, religious people have always terrorized other people in the name of their faith and instances of modern-day Christians slaughtering and terrorizing people still exist around the world. Since Franklin Graham has little to do with those instances and since we all know it's unlikely that the Christian students of Duke University have little to do with those attacks or with the KKK, they are then allowed to use the space without limit—as they should.
Both Duke University and the United States of America expressly support religious pluralism. However, when we begin selectively holding members of one faith accountable for every member of that faith, we must do this with all faiths.
You and I know that'll never happen.
When Duke bowed to the pressure of Franklin Graham, it drifted into a subtle bigotry and pushed its Muslim students into a form of second-class citizenry in which they are now forced to use the grassy area outside of the chapel for prayer instead of the chapel itself. In may ways, this echoes the days in which African-American Christians, who actually proclaimed the same faith of white Christians, were forced to sit in church balconies and even prohibited from entering certain religious buildings.
It's not right and Duke University has dropped the ball on this one.