It can differ but many insurance companies like to list the driver as the primary on the vehicle that that he or she drives the most, though they are covered to drive the other household vehicles as well (as long as no exclusions are on the policy). It appears your insurance company is such a carrier that requires your son to be listed as the primary driver on the car that he primarily drives and that is not unusual.

While this is typically up to the insurance company to decide if they match up the different drivers with the different vehicles that they drive the most, to find out if this is mandatory in Massachusetts you can contact the state's insurance regulatory body. In MA this is the Division of Insurance and can be contacted online or by calling their consumer hotline at (617) 521-7794.