Gulliver's Travels is often seen as an indictment of humanity as the dominant civilized and intelligent species on Earth. Although Swift spends much of the book satirized specifically-English culture, by the fourth book (written before the third, but placed last) he is viciously attacking almost every convention of human society. The idea that the Houyhnhnms have a perfect culture based entirely on logic all-but eliminates the possibility that Humans can attain the same status; depending on which psychological model is followed, Humans depend on logic for half or more of their reasoning.
And is there less probability in my account of the Houyhnhnms or Yahoos, when it is manifest as to the latter, there are so many thousands even in this country, who only differ from their brother brutes in Houyhnhnmland, because they use a sort of jabber, and do not go naked?
(Swift, Gulliver's Travels, gutenberg.org)
This streak of misanthropy runs off-and-on through the novel, and has often been interpreted as meaning that Swift was specifically writing a book of anti-human principles and themes. However, since human achievement -- even the silly achievements of the Laputa scientists -- are upheld objectively as great, it is more likely that Swift was aiming his pen specifically at the people in society who destroy rather than create. The quote above refers to people who, in Gulliver's view, are as Yahoos because they have no greater purpose in life; Swift's message, then, could be interpreted as criticism of under-education and lack of ambition, both of which cause failure of life and often of larger society.