A common myth is that the better shape a person is in will mean they have a faster or better metabolism. This can be somewhat true if a person has added some muscle mass to their body since muscle does burn more calories at rest than other types of tissue like fat but the amount of calories the additional muscle burns at rest is not as much as people often give the added muscle credit for. For instance if you were to convert 10 pounds of fat into 10 pounds of lean muscle while remaining the same body weight, you would burn around 50-60 calories more each day then before you converted the fat to muscle. Seems like a lot of work for very little additional caloric burn. But think of how much better the muscle looks on you over the fat :)
One fact that will always be true is that when you exercise you burn calorie and the more you exercise the more calories you will burn but this is not about that. This is about what happens to your body when you get in better cardiovascular shape from all the activity you are doing during exercise.
When we get in better cardiovascular shape our heart will beat slower at rest and during activity. Our heart rate is a key factor in figuring out how many calories we burn during an activity so the faster your heart beats while exercising the more calories you are essentially burning during a given duration. If it is beating slower than you burn less calories. In other words when you are out of shape and working out or exercising for an hour with an average heart rate of say 140 beats per minutes versus when you are in shape performing the exact same workout with a heart rate of 110, you will burn more calories in the same hour if you where out of shape.
This is simple just a byproduct of what your body does when you tell it you need to be more active, your body just gets better and more efficient at being active because that is what you are telling it to do. So a more in fit version of yourself will need to workout or exercise longer and harder to burn the same calories as a less fit version of yourself.
Watch my YouTube video for an analogy I use and also how I found this out from personal experience while I was prepping for my Fitness Shows.