The Ugly American is a reflection on the Pacific theatre of World War II and the emerging war with Vietnam. Since this novel was written in 1958, it deals with both the causes and the effects of the American attitude of east Asia. The central question is, "Did the Americans treat foreigners like humans?" And unfortunately, the answer is no, with one Christ-like example, the Ugly American himself.
Why Christ-like? Because he is despicable. Because he is ugly, he matches the Old Testament understanding of the despised scapegoat. And in the context of the vignettes, the courageous humanity of the ugly American leads him to fearlessly engage in the foreign culture, living in the village, for one, and investing himself by teaching the natives how to farm more efficiently and by teaching them to preserve foods for out-of-season. In other words, he brought a new way of life to them that would help them to flourish.
Unfortunately, the Ugly American is the minority, and the other vignettes describe the frustrating condescension that Americans became known for in the Pacific theatre. These are the loud, pretentious Americans who take their whiteness as an indication of superiority and create a serious rift between entire cultures. Even today, Americans are regarded in this manner.
So here's the central meaning of the stories: most Americans in east Asia behaved themselves so inhumanely and condescendingly that entire cultures became hostile to them, which might not be such good news in light of the unfolding conflict with Vietnam. And also, those who love people will be regarded as good, no matter what their background is.