When you think about the steamship, railroad, and telegraph in this book, think technology and progress, since this is what these things mean to our main man Manjiro. They are everything that Japan isn't in the 1800s, so they symbolize American intelligence and power.
But Manjiro doesn't just think that all these new advancements are awesome. He's torn:
It was hard to imagine anything changing this remote village, but the wind of change was blowing, and Japan would be swept along by it one way or another. She, his beloved country, had spent hundreds of years living from full moon to full moon while the West had sped ahead in science, invention, transportation, navigation, and, most ominously, military strength. There were hundreds of ways Japan would benefit from the coming changes. And hundreds of ways she would not. (5.41.3)
On one hand, all this progress is awesome. But on the other, it's the destruction of an older, maybe more peaceful, way of (Japanese) life. See, Japan at this point is at the tail end of the Edo period, a time of deep isolation for the country, so while other countries (like China) are all open to foreigners, Japan is the exact opposite.
There are some real perks to Japan's closed borders—no foreign invasions and no Opium War, to name a few—but Japan also missed out on some of the innovations of this time, technological developments that made other countries (like America) more efficient, wealthy, and strong.
By the way, if you get a sense of foreboding in the above passage, you're not wrong: "There were hundreds of ways Japan would benefit from the coming changes. And hundreds of ways she would not." Note the "would not"—the writer is signaling the future and what technology will do to Japan.
Think: bullet trains, super-tiny electrical gadgets, the Toyota Prius. But think also: World War II, the atomic bomb, and total destruction of a nation.
There's not a lot that can be done about all this "wind of change"—like nature, it's inevitable. It's also like the locomotive: It keeps chugging along, in forward motion, whether the world likes it or not.