Tolkien wasn't 'all black and white' and nor does Pullman present a world where there is no trust or hope, so the statement made in the programme wasn't really correct in terms of detail. However the books have a broad 'feel' that can be described in that way; how much this is intentional in terms of what the authors intended is a moot point. I happen to think that the difference is down to style rather than down to anythign each author was trying to 'say' or 'represent'.
Tolkien was attempting to write a story which echoed folklore and myth, which operates in broad strokes, whereas Pullman writes in the modern style (post-Austen, you could maybe call it?
) which goes into characters' minds. This is why Tolkien appears to have written a black/white story and Pullman a more grey one. However, get into the detail, as I say, and things are very different...
What is interesting is that until recently, we knew who our 'enemies' were - in as far as we can be instructed by our masters exactly who to despise this week or next
- in Tolkien's day it was the Germans or the Russians. Today we are told to hate someone new every day so we have no idea who 'the enemy' are, and it often turns out that the enemy is ourselves (how often do you read the newspaper to find out, for example, you are a scumbag because you gave your child cows' milk before the state sanctioned age of 12 months, or you do not deserve medical treatment because you like eating burgers).
I think that the difference is that Tolkien is able, through the style he attempts to use, to tell us who is good and bad, and the ambiguities stand out all the more for it; whereas Pullman's style does not permit such didacticism, in fact it's essential that the reader must decide for themselves.
Though I actually feel slightly more anxious if I am told who to hate. If everyone is bad, including me, then it's not such a problem