there are many "walls" - in Berlin, in Palestine, Weeping Wall in Jerusalem, execution wall in prison, wall of arrogance and misunderstanding. I don't think Roger Waters can be labelled as "anti-Semitic person", he's more intelligent than that.
btw, "the Wall" was written in 1977-1979 - the hiatus of Cold War and prime time of Arafat and intifada.