They booed at the end of Godspell's Day By Day because of the cross
Everyone was really enjoying it besides Amy's character.
And they only turned against the performers when the cross was lit.
It's a joke about how Jews are against Christianity.
Everyone looking pleased during the performance is the smoking gun.
The lit cross is focused too much to not be the cause for the booing.
Plus that's a way better joke than "crap gets applause - talent gets jeered".