No one was 'standing for the flag'. It was a standing ovation for the show. The man in question was sat in the front row.
It's by no means compulsory to join in a standing ovation for a show, but its the socially acceptable thing to do - especially if you're in the front row. Its definitely making a statement not to.
The Comedian should but have asked why - that's rude, and his outburst was even ruder. However, he was not chucked out for being Jewish - there's not even an indication the Comedian knew this.
It was unacceptable behaviour from the Comedian, but not antisemetic.