When a doctor tells you to quit drinking coffee because it is bad for whatever ails you, you do not have to take him at his word for it. The Internet makes multitudes of information on studies and health information easily accessible and you can usually find the information regarding these claims. You can then assess for yourself if the risk is real. Chances are your doctor never actually read the study, he just had heard about it. I'm not trying to paint doctors with a broad brush here.
Most doctors perform their task well.
The problem is that the media has put a lot of people into scare mode and they are running to their doctors anytime they think that something they are doing will make them likely to contract some disease later on. Imagine how many patients a doctor could see per day if he had to look up every one of these claims. I am not saying preventative medicine is without merit. Obviously, not smoking reduces your risk for lung cancer. Lowering your fat intake will help keep your weight down.