There seemed to be an equal amount of cheers too.
People generally don't like confrontation or conflict. Such a blatant assault on a sitting senator is a bit of a shock, even for someone like me watching comfortably in my living room. I'm sure many perceived this as a breakdown of decorum - and those are the ones McCain appealed to with his "beneath me" line. So with that context, the fact that the audience was even partially supportive is fairly encouraging.
For McCain's part, he played the only card he had, and that's deference to authority. How else can you defend supporting Alqueda?