The title poses an interesting interpretive dilemma to the reader. What is the symbolic meaning of The Last Unicorn and her story through this magical kingdom? One obvious place to start would be to liken the unicorn to nature, which is suggested when she realizes that humans have stopped seeing her as a mythical symbol and have started seeing her as a horse instead. This parallel connection between regular horses and the mythic unicorn points to the broader theme of the story, which is the sacredness of animal life and nature.
For instance, when the unicorn is captured, she is humbled, reduced from her immortal, sacred nature to an object of capture and fetishism. The humans flock around to observe, but not like a religious relic, nor as a sacred wonder, but instead, the humans are merely interested in entertainment. They abandon the sense of wonder that the unicorn is used to, and she must revolt and have her vengeance on the witch (a magical human, interestingly) for her freedom.
Now both horses and animals have been shown with sacred, mythic counterparts, and the unicorn is free, but perhaps the best symbolic explanation for the plot's meaning is actually to return to the first scene where the unicorn appears. In that instance, she is using her magic to stop humans from killing animals in nature. Her desire for life and freedom, and the mythic value of her existence, help paint a thesis statement in the novel, that nature and animal life are sacred and worth protection.