Most critics assume that the reason the Major is disgraced by the end of the story is that he is an officer in the British army during a time when many people in Massachusetts were beginning to turn against the British. Robin doesn't talk to him partly because he doesn't want to reveal his close connection to the major, lest he become the object of hostility, too.
The fact that you find the ending of the story difficult to interpret is not surprising, since many people have felt the same way. I've tried to explain that phenomenon in an essay on the story. Here's the link:
And here are the relevant paragraphs:
Even (or perhaps especially) when the narrative ends with the eventual appearance of the Major as he is pulled, “in tar-and-feathery dignity,” in a cart in the midst of a howling, hooting mob (85), ambiguities abound. How much sympathy (if any) should we feel for the Major? What, precisely, has he done (if anything) to deserve this kind of treatment? What specific political issues are at stake in this scene of insurrection? What should we make of Robin’s own “shout of laughter” (86) as he witnesses the painful humiliation of his kinsman? All these issues have been endlessly debated, with commentators staking out multiple and often strongly opposed positions and offering masses of often contradictory data in support of their claims. Hawthorne, of course, could have prevented much of this debate by making the “point” of the story clearer, especially its political implications. Is the story pro-revolutionary or skeptical about the revolutionists, or does it stake out some sort of middle position? Does Robin profit from his experiences in the city, or are they merely disillusioning? Does he eventually return to his country home, or does he stay in the city and “‘rise in the world without the help of [his] kinsman, Major Molineux” (87)? And what, precisely, should we make of that famous final sentence? How, if at all, is it relevant to any sort of national political allegory?
In the end (as indeed throughout the tale), Hawthorne’s main purpose seems to be to raise questions rather than to answer them. The “point” of the story has been – and will probably continue to be – endlessly debated in part because Hawthorne deliberately refused to make its “point” (or points) clear. He seems to have been less interested in communicating a political or moral message than in creating an aesthetic or psychological effect, and that effect is continually one of provoking, intriguing, frustrating, and puzzling both his protagonist and his reader. By the end of the story, we know little more about Robin or the Major than we did at the beginning, but by that point we have been made – through Hawthorne’s skillful artistry – not simply the witnesses to Robin’s journey of exploration but also its co-participants.