Don't criticise the doctor. If you had not been wearing a helmet he would probably and quite properly advised you do so in future. It is what many do (like advising you to drink less if you are over the 10 unit limit). he was being socially responsible.
This is because the doctor is acting on the advice of his professional association - the BMA. They have published a pro-helmet policy document backed up by the DfT and quoting the Cochrane Review:
http://www.bma.org.uk/health_promotion_ethics/transport/promotingsafecycling.jsp?page=5
Cochrane is generally regarded as the 'gold standard' of peer reviewed scientific research. So, by default, the doctor believes he acting on the best advice available.
Of course if you look into this research a little deeper things begin to unravel. Its best documented elsewhere if you want to Google search.
Fundamentally the problems are not about the report being wrong but is it answering the correct question? does it discriminate between different risk groups? is it applicable here? and much more. That is not something Cochrane can tell you.
The counter stuff (perceived risk, discouraging cycling causing greater risk to those that do etc) is hard to get good research on - and so it is not possible to definitely say helmets are not a good thing. The real problem is a lack of good holistic research in the field. Which is why statisticians who have looked into this area have mostly concluded 'case not proven either way' so choice is the very sensible current option in this country ...