I would think that the question should be "which insurance companies covers flight physicals", since it's the insurance company that decides, not the doctor. At least that's the way that I understand (sort of) the system.
I could be wrong though...it's happened often enough in the past.
My insurance pays for one work related physical a year. The doctors office won't file it since they don't think a flight physical is work related (you know, since I fly for a living and all). I file it myself and get reimbursed.