William,
I understand your logic but you have to view it in relation to biology - especially human biology. Take apes. They are some of the most muscular animals on the planet. Their diet is 100% fruits and vegetables. Look at bulls and horses. They are not carnivores and they are very muscular and they eat mostly grains. Now granted they have to eat continuosly as the nutritional denisty of their diet is not like humans as omnivores. They have a different digestive systems which is longer and in the instance of bovines has 2 stomachs. This provides a larger surface area and longer digestion time to help the body extract every last nutrient it can get.
Fruits and vegetables have fats and proteins. The amounts vary dramatically which is why vegetarians have to eat a very wide selection of foods to make sure they get all the protein and fats they need to sustain their bodies. You can't view a calorie purely on a macro nutrient level. Micro-nutrients are more important than macro nutrients for without them the body can't absorb and utilize your macronutrients. This is where fruits and vegetables are king as they are 90% micro-nutrient dense and 10% macro nutrient dense. Most disease states including cancer are actually diseases of malnutrition at the MICRO-nutrient level.
The calories they provide do contribute to total calorie expenditure therefore they need to be counted in your overall meal plan. A calorie is a calorie regardless of its nutritional "density". This is why people who drink diet soda actually get fatter than people who drink regular soda. The reason being is people don't count the calories diet soda has and coincidentally neither does your brain. This leads to overeating - which is taking in more calories than you need - which leads to weight gain. This same phenomenon will happen with a meal plan if you set a target caloric intake yet ignore calories coming from fruits and vegetables. I agree fruit is beneficial and when eaten in moderation can still help someone get lean. The main difference between fruits and vegetables are their glycemic index. Fruit contains fructose, an especially sweet sugar, which gets processed differently from glucose and is metabolized in the liver. This is why food companies make high fructose corn syrup - it is much sweeter than sucrose (table sugar). Vegetables contain glucose so their metabolic pathway is diferent from fruit. This is why people can get fat eating too much fruit but not when eating tons of vegetables in their natural state :-)
John