Longer barrels allow more powder to burn, resulting in higher bullet velocity. Higher velocity = less drop at any given distance. Most people like the idea of as flat a trajectory as possible.

However, many short barrel guns are extremely accurate. I always hear about guys having great 100 yard groupings with short barreled guns. Their trajectories may not be as flat as other guns, but for a muzzleloader, taking reasonible shots, they are just fine.