Ghee is considered a carrier for nutrients as well as medicines, throughout the body. It is used to lubricate the body channels - from the major channel of the digestive system, all the way to the subtle channels known as srotamsi (similar to meridians in Chinese medicine).
By keeping channels clear, ghee supports both nourishment via absorption, as well as cleansing and release of wastes and by-products.
When you consume ghee you are supporting the health of these channels. In Ayurvedic cleansing procedures of Panchakarma, larger amounts of ghee are consumed along with medicinal herbs, to prepare the body to eliminate toxins (ama).
We have a similar (though more subtle) effect by including ghee in our diet on a regular basis. Ayurveda recommends 2-3 teaspoons of ghee with your daily meals.