"Rikki-Tikki-Tavi" shows man (and woman) in a really awkward place within the natural world. On the one hand, Teddy and his family are obviously super into nature. Teddy plays in the garden and the family takes in Rikki-tikki—a wild creature, mind you—without much hesitation. On the other hand, nature just seems out to get them. Three snake attacks in less than three days? That's got to be a record. Then to further complicate matters, the only way the family can protect themselves from nature as represented by the cobras is by domesticating a natural creature like Rikki-tikki. Perhaps the story's view of nature can best be summed up as: "Wow, isn't nature wonderful? Sure hope it doesn't kill us."
In "Rikki-Tikki-Tavi," the division between man and the natural world is also a division between Imperial Britain and India, with the British Empire and civilization on one side, and India and nature on the other.
It's possible to read "Rikki-Tikki-Tavi" as arguing that the man's ownership of the garden is a result of survival of the fittest (a relatively new idea when Kipling was penning the story).