The unifying theme in Gulliver's Travels is size and how Gulliver encounters people much bigger than him (such as the Brobdingnagians) and much smaller (such as the Lilliputians). The way in which size interlinks with morality, then, is that size means power: Gulliver could easily crush the Lilliputians, and the Brobdingnagians could easily crush the comparatively tiny Gulliver. When these large beings show themselves willing to speak to, communicate with, and be sensitive towards the much smaller people in their company, they demonstrate their moral fiber.
Consider, for example, the way Gulliver reacts to the Lilliputians' attempts to pin him down. Of course, he does contemplate squashing them, but ultimately he decides it would be better to try and reason with them, and this leads to a fruitful relationship. In the same way, the farmer who finds Gulliver in the land of the Brobdingnagians tries hard to understand what Gulliver is saying, and so Gulliver is able to survive (even though the farmer does partly consider what benefit he can derive, financially, from his little toy).
By comparison, other large creatures, such as the king of Laputa, demonstrate how power and size can be used in an immoral way which is ultimately unhelpful. The king of Laputa thinks that he can wield power simply by making himself bigger than the people he wants to oppress. Ultimately, however, this is shown to be an unhelpful way of exerting control, and it does not cause his subjects to respect him.
Swift's satirical approach sets out a very serious point about power, morality and corruption. He is suggesting that the use of physical might to try to rule over smaller and less powerful people is a sadly common way to rule but not a very moral one. The best relationships in Gulliver's Travels are those where there is mutual respect, regardless of the physical power imbalance.