I am surprised the doc recommended not getting the vaccination. I live in New York, and as of this year if medical care professionals don't get the shot, they have to wear masks while caring for patients.

Personally, I think the fact that some people get the flu after getting the shot is not really proof that the shots don't work. It is true that not all strains are covered, but clinical trials have shown that the risk is lower for people who get the shot. Clinical trials are more reliable evidence than anecdotal observation. Doctors are supposed to be moving towards "evidenced based medicine."

That said, whether or not a particular individual get the vaccination depends on their own health status. Don't forget the clinical trials probably only include healthy people.