Perhaps the portrayal of this message (and the tiny hint of San and Ashitaka's romance and Moro's views on nature) was what made the film so touching to me. Another wonderful aspect of the plot is that it sends a message - Protect the Earth and all will survive in peace - a message either discreetly or strongly portrayed in many of Miyazaki's films.
Although it her actions were environmentally damaging and wrong in general, she did it to help her people survive which is what all the species on Earth strive for. Even Lady Eboshi the most antagonist character in the movie had a reasonable motive for trying to get rid of the animal gods and cutting down the forest. There were no complete "good" or "bad" guys. Since it was a Studio Ghibli film dubbed by Disney I liked the fact that it wasn't a "they all lived naively ever after" film. The first time I saw Princess Mononoke I was completely moved and surprised. This is truly an adult work: children might like some of the visuals, but I doubt that many kids below teen age will have any idea what it is all about, and even adults will get more out of this each time you see it again. His work has a depth and sophistication that goes beyond Disney cute. Some say he is the Japanese Disney, but I don't like that. If you haven't seen Miyazake, give it a try (but maybe look at Sen to Chihiro first, or even Laputa or Kiki's Delivery Service, for easier and lighter introduction to his work). The English translation drew on some good talent but they seem not to have "gotten it" quite so intensely as the Japanese crew. Japanese television documented a lot of the production. The original Japanese soundtrack has some amazing singing and draws upon some of the best talent available for voices - in Japan, Miyazake is universally known and this was a masterpiece carefully crafted.
There are at least half a dozen well developed characters threaded through the story, and their animation is wonderful in displaying subtle character. And, continuing the trend to be more personal, concerned with ethics and character, and less sci-fi. The animation is spectacular, and unusual, with new elements even for Miyazake and marks a new departure for style which you can see continued in his next film, Sen to Chihiro - more nature, more wild, more jamming on elements from Japanese myth and folklore. It has many Japanese mythic elements but even then, it is a work of Miyazake's unique imagination, and is not intended to be simple or to have a clean resolution. The Princess (Hime) of the story is a mysterious human who has been raised by wolves (which are themselves powerful forest gods, a little reminiscent of the Amerindian Coyote myth), who becomes both his ally and his enemy.
But this is not a simplistic tale, he finds there are other characters in play, and there is good and evil in everyone, and no easy balance. The evil controlling it transfers to him, beginning a slow takeover, and he must journey to the origin of the conflict to find a way to cure himself and incidentally, as he will learn, to try to restore balance. The world is not in balance, and a distant conflict between industry and nature has wounded one of the gods of the forest, which is then killed by a sentry boy as it rampages into farmland he guards. It is set in an imaginary time which blends the time of the ancient gods (Shinto style, gods of place and nature) with the settlement of humans and the coming of metalworking and war. This seems to be Miyazake's most personal work, clearly a serious design.