I think that often, the doctor doing the un-recommending doesn't understand the sport. I had a neck injury last year that required surgery. Chiropractor (in all other respects a decent egg) is one of those people who has the "hide in a padded room to stay safe" outlook on life. She told me that I shouldn't ride long distances because of my neck - I guess she's seen a few cyclists come through her practice. What she didn't understand was that I was going to be meticulous on fit, and that I was going to make sure I wasn't in a super aggressive position, and that I was going to take the training slowly and listen to my body (I tried to tell her all these things, but she would have none of it).
I got the bike in late September, have been training for a century since February, and my neck is stronger than ever.
"Susie" - 2012 Specialized Ruby Apex, not pink/Selle SMP Lite 209