The last section of Gulliver's Travels is partially a satire of race-relations in European society. It would have been easy to show the superior race as, for example, a darker-skinned race that Gulliver discovers ruling over whites, but that would have been obvious and too easy for a writer of Swift's skill. Instead, he uses a common beast of burden that no person thinks of as intelligent, the horse. Horses have been domesticated and used for labor for centuries, and to show them as the rulers of a Utopian society is to call into question every assumption of modern science. Gulliver is astonished, even ascribing the Houyhnhnm intelligence to magic, but quickly finds himself drawn into the Houyhnhnm's society of peace and non-conflict.
[I] wondered more to see the rest employed in domestic business... However, this confirmed my first opinion, that a people who could so far civilise brute animals, must needs excel in wisdom all the nations of the world.
(Swift, Gulliver's Travels, eNotes eText)
His assumption that a smart animal must have an even smarter human master is quickly corrected, and Gulliver discovers that he himself is considered to be little more than a smarter-than-average Yahoo. By changing all of Gulliver's preconceptions about how humans and animals interact, Swift challenged 18th century readers to examine their own prejudices and wonder if they are based in anything but societal norms and indoctrinated bias. A horse, as a creature that most people take for granted as domestic and used for human-centric goals, is a perfect metaphor for any assumptions that people make about other people, whether it be for their race, religion, or gender.