I think there are several messages in this story that can be classified as the main message. I definitely think the story contains a warning about technology. I teach a media studies class to high school seniors, and the class examines something called "The Myth of Technology as Protector and Savior." In short, this idea states that technology is by definition beneficial. I think much of the general population believes this, and I think this has helped to propel the pace of our technology developments in the last 100 years or so. What's interesting is how many science fiction writers warn against such assumptions. The Time Machine is a story that does this. Through the Eloi and Morlocks, Wells shows readers that technology could eventually result in the undoing of society and mankind. The book shows us that while technologies can lead to great progress, they can also lead to violence and intellectual stagnation.
I believe a second main message of the book is a message about social class and inequality. Again, the relationship between the Morlocks and the Eloi is used to convey this message. The class distinction between these two groups is stark, and Wells uses it to point out the inequalities that he saw in Victorian England. Wells's story takes the real world social issue to a terrifying conclusion by showing that perhaps it is leading to the development of two completely different human species. Perhaps that is not a problem for many, but Wells creates the two groups in such a way as to show readers that each group ended up having the worst characteristics of each initial group.
As is often the case with Wells, one of the dominant themes of this novel is the use—or rather, abuse—of science and technology. Scientific and technological progress are all well and good, but Wells is at pains to point out that they also have a dark underside. At first, The Time Traveler thinks that the Eloi have been liberated by technology, free to pursue a life of ease and comfort. However, he soon comes to realize that there is another side to the story. Not only has technology not been used to liberate the Morlocks, it has also rendered the Eloi apathetic and vulnerable to being eaten by the Morlocks.
The Victorian era was a time of rapid scientific and technological development. Belief in progress was almost universal. What Wells is trying to do in The Time Machine, however, is to urge people to take time to see what is going on around them and to see where all this astonishing progress might lead. Wells is not someone who wants to just turn the clock back to a simpler, more primitive past, and he is not opposed to scientific progress in principle. He just wants his Victorian audience to be aware of its potentially negative and destructive consequences. He is especially concerned that if things continue on their present course, then humankind will experience a kind of evolution in reverse; we will be reduced to a state of tranquilized contentment like the Eloi, and we will lose what is distinctively human in the process.