Did you ever discuss in school whether humans were animals? We imagine Wells would say, "of course humans are animals – but a special kind." In The Time Machine, there is a fairly steady tension between these positions: either humans are just another part of the natural world (just another animal), or they're special.
There are arguments for each of these positions in this book: for instance, humans evolve like other species, but they can also direct evolution (see 4.25). This is a serious issue for the Time Traveller, who witnesses both increasing human control over nature and nature's continued control over humanity. That is, people may make new technology that changes the environment (Humans 1, Nature 0) – but then they evolve in reaction to that changed environment (Human 1, Nature 2). So humans might be special, but not that special.
While humans can harness the forces of nature for small projects in The Time Machine, the major forces always remain outside human control.
The Time Machine shows that natural instincts will always trump education and training. Even though the Time Traveller is a scientist, he reacts to the Eloi and the Morlocks instinctively.