Do you need a tune for a bone stock 2001 Cobra? No... You can get a few additional HP/TQ out of your stock setup though if you were to have it tuned for max performance.
When you read about people recommending a tune for a specific car it's usually the result of the owner changing some aspect of the engine. This could be as simple as adding a cold air kit to as extreme as replacing the cams. A good rule of thumb is that if a specific mod affects the way the motor sucks in air/fuel or pushes out exhaust, then a tune may be in order. For example, if you were to add a catted mid-pipe and a cat back exhaust to your stock '01 Cobra you would not be required to change the stock tune in order to see a performance gain from these parts, but... if you did have it specifically tuned to take advantage of the cars new ability to more efficiently exhaust the spent gases you'd realize a larger gain from those modifications.