Researchers have been trying to answer this question for quite some time. Although the results are not conclusive, and more research is needed, here is a study and an opinion on the matter.
Between 1993-1996, 133 whiplash patients and 233 healthy subjects participated in a whiplash study. 10 years later, the same participants performed in a follow-up study. Although the whiplash patients showed significant improvement in their pain levels, many of the symptoms still remained. During the study, the whiplash victims were more likely to experience pain in each of the symptoms evaluated than the healthy subject group. Unfortunately the MRI scans could not explain the higher prevalence of pain.
I believe the reason the pain lingers is because the original soft tissue was greatly damaged during the accident. Depending on the extent of the injury, and the extent of the care and therapy after the accident, the soft tissue damage may never fully heal. This area then becomes a weak point for all future injuries and inflammatory conditions. That is why I highly recommend you listen to the doctor and follow through with your care in order to ensure the least amount of residual pain and problems in the years to come.