First, you need to understand that there are MANY different types of protein drinks. It all depends on your goals. You have shakes to gain weight loaded with calories and carbs and you have low calorie shakes with no carbs.
There are POST workout shakes that are loaded with fast acting proteins, and there are shakes you drink before bed that are slow to break down through the course of the night.
Once you understand your goals, you can choose the right supplement for you.
The general rule of thumb is that REAL food is always option one, but for someone like me that tries to consume nutrients 6 times a day, its just not realistic. This is where using shakes as supplements to get that protein in comes into play.
Our muscles need to be fed, and the ideal muscle food is protein coming from many different sources...meats, dairy, whey, etc...
A popular misconception is that if you drink these shakes, you will suddenly transform into a bodybuilder...WRONG! Again, its just another source of nutrients, no different then eating some grilled chicken.
I personally have a low carb whey protein shake between breakfast and lunch, and a Meal Replacement shake with a good distribution of calories/protein/carbs right after my evening weight lifting session. Sometimes I will have another lo carb shake right before bed, depending on if Im trying to put size on at that particular time in my training.
You should look at your body like a car and the food/shakes are the fuel to run that car. Sometimes you use 87 Octane and sometimes you use 93...it all depends on your goals.