For a medical office visit, reimbursement covers the physician's time and also the overhead involved in maintaining the office. When that visit occurs in a hospital owned clinic, the reimbursement is split. The physician gets paid for their time, and the clinic gets paid for the overhead.
The physician gets paid less for a visit that occurs in a facility setting, because they aren't getting paid for the overhead. You'll notice on the Medicare Physician Fee Schedule, there's a Facility Price and a Non-Facility Price for each office visit code.
Example: 99214 - Physician in a non-facility setting would be paid $129.77. However, the physician in a facility setting would only be paid $98.97.