Gulliver takes a lot of time to situate the different imaginary islands he visits: Brobdingnag is in the Pacific, between California and Japan. Lilliput is off the coast of Van Diemen's Land, what we now call Tasmania. But the one place that Gulliver actually visits during his travels – at least, the one place that is both real and not England – is Japan. As Gulliver is planning his route home from Laputa, he travels from Laputa to Balnibarbi, the continent below it, and then northwest to the island of Luggnagg, and then northwest again to Japan. From Japan, Gulliver manages to get passage to England by pretending to be a Dutch merchant (remember, he studied medicine at the University of Leiden, which is in Holland, so his Dutch is fluent). So – why Japan?
We can't say for sure, but we can think of a couple of historical reasons: one might be that the real object of critique here is not the Japanese, but the Dutch. And following the beginning of the Tokugawa shogunate in the early seventeenth century, Japan closed its borders to all European traders except the Dutch. Even the Dutch were only allowed to live in a small enclave in the southeastern city of Nagasaki, on the island of Kyushu.
So, Japan provides a useful place for Swift to take Dutch behavior out of context, to criticize it without having to provide the degree of description that he lavishes on all of his imaginary places. Japan itself appears completely mysterious to Gulliver – it's the one land where he doesn't make any attempt to learn the language. So, he passes over it in exactly one paragraph in Part 3, Chapter 11. Posing as a shipwrecked Dutchman, Gulliver uses his letter of introduction from the Luggnaggian King to ask the Emperor of Japan for the right to travel to "Nangasac," presumably Nagasaki, to rejoin his countrymen.
The speed with which Gulliver skims over a real foreign country, Japan, to get back to telling tales of fake foreign countries might emphasize that the target of Swift's satire is closer to home. In the middle of a boom in traveler's tales, which tell stories about the weird and outlandish behavior of foreigners, Swift is telling Europeans as a whole, and the English in particular: "Ha! You think they're so strange? Look at your own customs. Now those are weird."
Speaking of Japan, we can't forget that the way that Gulliver first gets marooned and then taken up to Laputa is through a run-in with Japanese pirates. In fact, numerous pirates of the South Seas were Japanese, though the heyday of Japanese piracy was a bit earlier than Swift's time, in the late sixteenth century. Japanese pirates provided a real threat to Portuguese, Dutch, and Chinese traders off the coasts of China and Southeast Asia. So, here's an odd bit of real realism that mimics the fake realism of Gulliver's observations of Lilliput, Brobdingnag, and so on. It's like Gulliver's playing a game with us: we read along happily thinking that everything we're learning about is fiction, and then boom! Suddenly there's a mixture of historical fact. Maybe Swift is reminding us that there's still a lot of truth in his satire, even when it looks totally made up.
So why does Swift seem to hate people from Holland so much? After all, it's not just Part 3, Chapter 11 that contains some pretty nasty stuff about the Dutch in it. There's also that malicious Dutchman in Part 3, Chapter 1.
And what's up with the specific form of anti-Dutch feeling that Gulliver expresses? Gulliver asks the Emperor of Japan for special permission not to have to step on a cross. The Emperor of Japan agrees, as a favor to Gulliver's patron the King of Luggnagg. But the fact that Gulliver doesn't want to trample the crucifix makes the Emperor of Japan "rather suspect [Gulliver] must be a Christian" (3.11.4) as opposed to a Dutch person. He thinks the two things, Christian and Dutchman, must be mutually exclusive. And when Gulliver reaches "Nangasac" posing as a Dutch merchant, all of his supposed fellow Dutchmen keep asking him if he has trampled the crucifix yet (3.11.5).
The opposition that Gulliver suggests between Christianity and Dutchness is the key to this particular satire. As a representative of a national church, Anglicanism, Swift did not approve of the Dutch policy of freedom of religion (source: Robert Greenberg, Editor, Gulliver's Travels. New York: Norton, 1961, 128.). Sure, he may not approve of wars between countries based on Catholicism vs. Protestantism, but that doesn't mean he thinks the state shouldn't acknowledge a national faith in Christianity. So, all of this oddness about stomping all over the cross, the symbolic representation of Jesus, may be a dig at the Dutch policy of not explicitly protecting Christianity as its national belief system.