This episode of Gulliver's Travels has probably been subjected to more analysis, or specifically psychoanalysis, than any other within Book IV or the entire tale.
A frequent view of commentators has been that in this scene, Swift is expressing his own revulsion towards sexuality and/or women. Gulliver is horrified over the "attack" upon him by the female Yahoo. It's always dangerous to engage in amateur psychologizing, but given what we know of Swift's personal life plus various other misogynistic passages in his oeuvre, this analysis seems to make sense. Perhaps, however, Swift's point is that Gulliver is actually aroused by the female, and because of this, he realizes he is no different from these savage, animal-like beings. A physical link (and specifically a sexual one), lacking before, has been established between the civilized and the uncivilized. Before this encounter, Gulliver has remained in denial over the fact that he and the Yahoos are the same species. His ostensible horror over the female is a transference of his own self-loathing, brought out by his response to the female and his recognition that she is essentially no different from women in his own civilized world.
One has to keep in mind that Gulliver's Travels is a satire and that Swift's technique, like that of other satirists, is to ridicule through parody and exaggeration. The Yahoos are a deliberately distorted version of humanity, a kind of compendium of mankind's worst traits. Swift did not "believe" that humans were all bad, and he is not attempting literally to equate real humanity with the Yahoos. Gulliver's revulsion toward the female is perhaps intended merely to emphasize the comic element in the story, and Gulliver's naive reaction may be an inadvertent form of self-self-parody by Swift. In one of his scatological poems, Swift mocks men who place women on a pedestal and who seem somehow to disbelieve that women are physical beings. The Gulliver episode is at least partly another instance of such bizarrely unrealistic attitudes on the part of men.