Hanna has the best piece on the subject, natch. Money quote:
You can probably guess how things turned out. Given enough time and effort, Hollywood can tweak and polish and recast even the darkest message until it would seem at home in a Fourth of July parade. In the end, the religious meaning of the book was obscured so thoroughly as to be essentially indecipherable. The studio settled on villains that, as Emmerich put it, “feel vaguely kind of like a fascistic, totalitarian dictatorship, Russian/KGB/SS” stew. The movie’s main theme became, in one producer’s summary, “One small child can save the world.” With $180 million at stake, the studio opted to kidnap the book’s body and leave behind its soul.