For me applause after a cruel joke haven't been confusing. As Kurt said, kids weren't brave enough to say what they think of him. They whispered behind his back and made him a Prom Queen. When he confront them, again, they haven't been brave enough to deal with it. If they hadn't applauded, Kurt would found out who took part in the vote. And not only him. Principal Figgins was on stage with Kurt. Students had no other option than accept Kurt's coronation and pretend they happy for him.