If natural progesterone is so wonderful, why isn't it used by my doctor?

Is it so? While there are some industry-based studies which suggest that natural Progesterone when combined with percutaneous estrogen is associated with a decreased risk of blood clots, most of the time it is the effect of Progesterone that is needed, and synthetic substitutes have this same effect on the receptors for the natural hormone.
Ask him/her. It's 'wonderful' for specific reasons only, it's not just something for everyone. I don't use it at all because most 'natural' Progesterone is not even progesterone. Ask your doc what he/she thinks?