There is no one message in The War of the Worlds, but several. However, for the purposes of answering this question, one could possibly whittle it down to this one: the dangers of technology. This is a recurrent theme in the works of H.G. Wells. The superior technology of the Martians is dangerous for the Earthlings because it allows the aliens to prevail in what turns out to be an embarrassingly one-sided conflict. Yet for all their advanced technology, the Martians ultimately lose, as they're wiped out by the Earth's bacteria, against which they have no defense.

Wells wants us to learn a valuable lesson from the Martians' fate. He wants us to understand that, however technologically advanced we may think we are, it's no cause for complacency. Technology can greatly enhance our lives and change them for the better. But it can also do great damage. It is often also woefully inadequate in meeting our present needs. This is the situation in which the Martians find themselves. They've developed sufficiently powerful, sophisticated technology to help them invade and subdue an entire planet. But when it comes to dealing with what to humans are harmless bacteria, they're completely helpless.

Present-day scholars often interpret The War of the Worlds as an allegory of European imperialism, and there is some truth in this way of looking at it. However, in my view there are other more fundamental messages in the story.

Wells's basic point in this, and in his other science fiction, is that throughout history man has been limited and even delusional in his view of both himself and the universe. The idea that intelligent life might exist elsewhere in the universe was still a novelty in Wells's time, and would have been viewed as heresy by many or most religious believers, simply because there is no mention of such a possibility in the Bible. Wells was opposed to organized religion and what he believed was the narcissistic view of mankind that it encouraged. In The War of the Worlds the earth is shown as vulnerable not only to attack but to the possible enslavement of its population by extraterrestrials. The Martians are defeated by their own vulnerability to disease, instead of by either human force or some kind of divine intervention to protect humanity. Wells thus sees mere chance as the primary force operating in the universe.

Most contemporary analyses of The War of the Worlds compare it to European Imperialism and expansion; with their superior technology, the Martians (Europeans) invade the weaker nation of England (Africa, Asia, etc.) and dominate the "inferior" people with their military might. Wells showed how Humankind, believing themselves to be superior to all other creatures, can be reduced to animalistic survival instincts; in the same manner, European expansionists thought of other races as inferior, and considered their actions in those regions moral. If the Martians had no reason to consider Humanity as anything but inferior animals, they had no reason to spare them; using humans as cattle and food is similar to the enslavement of humans by other humans practiced around the world during past eras.