An interesting article at Scientific American asks the question Can Fat Be Fit? Indeed fitness actively improves body composition, increasing muscle mass, while also increasing bone mass. This increase in body density, if coupled with cardiovascular exercise compounds the improvements to increase overall metabolism. All of this snowballs to cause weightloss. Of course your weight is still day-to-day a factor of calories in versus calories out (burned).
I think this is an interesting discussion overall, and definitely worth a read. Looking at different sports, you see a different pattern of fat distribution, some extremely skinny and wirey, while others are softer. Sumo wrestlers might be an extreme example, as they are quite fit, yet continue to maintain significant bulk.