One important theme is that of class conflict. Wells himself lived at a time when industrialization was contributing to enormous class inequalities, and the time traveller discovers that a form of class division has persisted into the future in the form of the Eloi and the Morlocks. The traveller posits that the Morlocks evolved from the working class, and the Eloi the capitalists.
Another theme is that of technology. The turn of the century was a period when technological inventions were changing people's lives, especially in the cities. There was a tremendous faith in progress among elites. The Time Machine suggests that this faith may be somewhat misplaced. As he travels to 802,701 AD, he discovers that human beings have been replaced by other species of beings. Thirty million years in the future, there are no creatures at all except for a hideous blob with tentacles.
Finally, there is the theme of evolution, implied by the previous theme. Human beings have evolved into the Morlocks and the Eloi, as a result of their ability to adapt to their different surroundings. Each of these themes suggests a warning against overly-optimistic views of progress, underscored at the end of the book in a description of the traveller:
He, I know—for the question had been discussed among us long before the Time Machine was made—thought but cheerlessly of the Advancement of Mankind, and saw in the growing pile of civilization only a foolish heaping that must inevitably fall back upon and destroy its makers in the end.
The narrator feels differently, but the overwhelming message of the book can be construed as a warning against hubris and faith in progress.