What does calling someone an 'Uncle Tom' mean?

Yes, it's an insult. You'll probably remember how loyal and deferential Tom was. And that's sort of what the phrase means - a black person deferential to and seeking the approval of a white person. I think what you're seeing is the difference between how Stowe portrayed him and how he's perceived in a more modern context. I felt the same way after reading the book, too. I just liked Tom so much that I couldn't understand why it was bad to be like him.