With the prevalence of HMOs and Medicare patients, doctors are finding themselves in a position of working longer hours and having to take more patients. Your doctor now sees 6 patients an hour 9 hours a day and even having to put in the occasional Saturday. There is no way your doctor can devote the enormous amount of time necessary into discovering the validity of the thousands of these claims and be knowledgeable enough to advise you on them. Additionally, I seem to be hearing a lot of stories about doctor's treating their own advice as if they were the word of God. Medicine is an ever evolving science and while 8 years of medical schooling is worthy of respect, it does not make one immune to criticism.
Doctors are human, they make mistakes.
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.