Activist Eugene Doherty said: "Arab and Israeli children are segregated and we are opposed to that. Palestinian children are at risk of the things that the Israeli army do."
Among the fans rejecting the protest was Keith Fairclough, a member of the Merseyside Friends of Israel group.
"My feelings are that this was just another way of having a go at Israel," said Mr Fairclough. "It's a disgrace."
The match passed off without any incident, and with minimal police presence. England won the contest 5-1.