At least it's better explained than in the comic story they based it on! Man, her portrayal was random in that comic, damn you Loeb. We don't really see Amanda's organizations in the movie, but it is obvious she doesn't trust Luthor very far. Luthor seems to see them as kindred spirits, even before his grip on sanity starts to slip, which I guess if you are a megalomaniac is an easy mistake to make?