One my friends who has a history of sexual abuse always shares this information with the nurse and she or you need to relay it to the Doctor directly. It's best for you and the health care provider if you just put it out their an they can adjust examinations accordingly. If this is strictly a phobia explain clearly that you would almost stay sick than to have your pelvic area checked and if you think the Dr. hasn't really heard you then keep repeating the same message until he comments on your comment. You own your body and you have the power of being upfront with any health care provider. Plus you can refuse a treatment and if it's extremely important they are responsible for explaining why it's so important.
You can do this by thinking about his work from the professional point of view, than an ordinary man. It is all up in your mind, where the phobia is coming from. Believe he is doing so to help you recover from whatever sickness you're in.