Personally I think it's a perfectly valid question, but not for a GCSE paper - students at that level wont be doing near enough learning and research around the subject than they would at higher levels (either in lectures or on their own) to give a good answer, which in all honesty would probably require a good few thousand words on it (at least) to even get a basic answer - you're probably even looking at something which is a valid topic for a book there...
Anyway, yet again we've had another great line from the Education secretary... "to suggest anti-Semitism could ever be explained was "insensitive and, frankly, bizarre.".
The only way we'll ever overcome prejudice(s) is to look at why they happen and to try and explain them - it's not bizarre at all to look at the causes of things, as it is after all the search for truth (and the point of education...). By explaining why prejudice happens we can then seek to defeat it, simply saying "oh you can't explain it so it's pointless to try" - especially when we fear that we'll offend someone by doing so, is ridiculous - looking for the truth outweighs offending someone pretty much all the time in my opinion, and tip-toing around things because they're a sensitive subject doesn't result in credible answers for things being put forward. The man is correct to oppose the question I think, but he's done so in his typical retarded way.
Anyway - thems are my 2 pence.