This ^

The shuttle is optimized for business travelers on short (and often same day) trips. It has a set hourly schedule as people frequently catch earilier or later flights when meetings get out early, etc. I believe there is also a fair amount of walk-up and last minute bookings.

While BOS-PHL has an even greater frequency then the shuttle, it is optimized for people connecting and not as business heavy of a route. My guess is the schedule is more based on when the largest amount of pax are arriving or departing PHL.