Physician compensation is neither mysterious, mystical, nor complicated -- it simply is not adequately explained to (or understood by) students, residents, and even many attendings.
In the current environment you can either have a salaried, non-clinical career or one that directly or indirectly production / profit based. Even most "salaried" clinical positions are ultimately production driven -- if you a replaceable drain on the system, expect to be replaced. Unfortunately the converse is not always true -- hence the high rate of (productive) physician turnover at many institutions.
(Revenue - costs) = total compensation.
You have to take each factor separately in order to understand how the system works. Revenue is driven by volume, payor mix, and CPT mix. Peds suffers from social welfare blight (SCHIP, medicaid) and the undervaluation* of cognitive services; taken together, even with the high volume that many pediatricians see, the top line revenue numbers suffer. Costs are high due to the high volume nature of the specialty as well as some potential costly and low profit operations (vaccinations is the first thing that comes to mind).
*Notice that I did not say "relative" undervaluation -- many procedures are not "overvalued" despite the current drumbeat; the problem is simply that physician time and intellectual property are undervalued.