If you care about your long-term health, it is much better to get your protein (and all other nutrients, by the way) from an actual meal and not from a supplement, because of digestive issues:
In my opinion, if it's just about enhancing recovery after a workout, ideally you would eat any food rich in high-quality protein (chicken if you have access to grass-fed, pork, nuts if you vegatarian etc.) + some green vegetables (voluminous but low in calories, to supply fiber that will help digest the protein) and after the main meal maybe a grapefruit or orange (vitamin C speeds up recovery). If you look to gain weight, you can additionally eat more carbohydrates with the meat and also eat some carbs before the workout.
And what if we take protein supplements and don't have these issues? It sounds like it only affects a small portion of the population - just like pretty much any other food. How many people are intolerance of gluten, or lactose? Would you suggest bread or milk are bad for your long term health?
Besides that, if you ingest a protein shake and eat nothing for a few hours the toxic waste products of digesting the protein will stay in your bowels longer then with a richer meal.
http://en.wikipedia.org/wiki/Whey_protein#Digestive_Issues