The story is told through Gulliver's eyes and experiences; as he learns more about them, his opinion changes, and of course, so does the reader's. He learns to appreciate and see them as much, much more than the tiny little annoying people who originally tied him up.
Authors do not provide everything about all characters up front. Many characters are developed over the course of the text, providing more indepth information about their character.
That said, as readers learn more about the Lilliputians, the way that they feel about them can change. Think about it this way: When one first meets someone they make snap judgments about them (normally based upon stereotypes. It is not until one learns about another that they can honestly judge or characterize another. While one may have not cared for another initially, as they learn more about them, they may change their mind.