In reality there are many differences between the two. If your goal is to lose weight, meal replacement shakes are the way to go. One of the biggest differences between the two is calorie content and sugar content. Meal replacement shakes (such as HMR, Medifast or Nutrimed) are designed to be low calorie while providing essential nutrients. In effect they "replace" a full meal.
Protein shakes can be made from many different ingredients, however they usually contain a substantial portion of protein. If using a protein mix to make a protein shake, this is usually mixed with fruit, milk (or yogurt). This greatly increases the calorie content as well as the sugar content. Many commercial protein shakes are generally higher in calories and deficient in many vitamins and minerals.
If you are considering meal replacement shakes to supplement your weight loss goals, the consensus is to stick to products that are specifically formulated for weight loss. The protein/calorie/carb/nutritional value in these shakes have been tested and found to be an effective and healthy way to get you on the road to losing weight. Whether you are only replacing 2 or three meals a day or if you are doing a full fast - stick with shakes that are recommended by physicians and dietitians...HMR, Medifast or Nutrimed.