It is because lighter underbellies are more natural looking. We almost subconsciously want to make characters with lighter underbellies because of this.
For many animals (such as Great White Sharks, orcas, and penguins) a lighter underbelly is a form of camouflage. When looking at them from above, the dark color blends in with the dark ocean floor. When looked at from below, the light underbelly blends in with the sky above.
This trait seems to still be present in land animals, for whatever the reason. In nature, it's much more common to see an animal with a lighter underbelly than a dark one.
That said, characters with dark underbellies can still look good if you make them correctly. I have a few characters like that myself.