When you choose one way out of many, all the ways you don't take are snuffed out like candles, as if they'd never existed. - Philip Pullman

As for what it's against - the story is against those who pervert and misuse religion, or any other kind of doctrine with a holy book and a priesthood and an apparatus of power that wields unchallengeable authority, in order to dominate and suppress human freedoms.

We don’t need a list of rights and wrongs, tables of dos and don’ts: we need books, time, and silence. Thou shalt not is soon forgotten, but Once upon a time lasts forever.

When she saw how they worked, not on their own but two by two, working their trunks together to tie a knot, she realized why they'd been so astonished by her hands, because of course she could tie knots on her own. At first she felt that this gave an advantage — she needed no one else — and then she realized how it cut her off from others. Perhaps all human beings were like that.