Malpractice insurance for internal medicine (general medicine that I'm referring to) is ~$33K-$34K in NY area based on the link you've provided.
Now let's do the math to readjust my estimates.
One full time staff with $30/hr * 2080 hours in a year = $62400 => let's just double that to cover everything like their health insurance and liability insurance so each full time staff costs = $125000/year
2 staff * $125000 = $250000 Rent = $60000 (the doctors sometimes own the practice, but let's just assume it's a rental) Malpractice = $35000 EMR system like eClinicalWorks = $10000 (amortized for upfront and yearly costs; software like eClinicalWorks costs ~$600/month on average)
The total expense of running a primary care (internal medicine) clinic = $250000 + $60000 + $35000 + $10000 = $360000 (let's just say $400K/year)
When I said these clinics on average make $1MM/year (of course, they are all near NYC/NJ metro areas), I truly am underestimating the income these doctors get from each patient visit. As an example, if I visit my physician at NYU Langone for my yearly check-up (at most a 10-mins encounter), the net reimbursement from my insurance they get for my visit (after the insurance company's discount/rate negotiation) is ~$250 without including the lab fees. Out of emergency and convenience, I happened to visit one of these primary care clinic doctors where my wife used to work at, and the doctor charged me $80 (that was back in 2019) in cash for an ear infection check (total of 5-minute encounter) and that's because I paid in cash and because my wife used to work for her. All of these doctors that my wife volunteered at or worked for (she got paid $15/hr max from some of these docs) are making a load of money from these clinics because we know a couple of them personally as well.
Again, I'm not saying you are understating the profit margins. You probably have been working with the clinics in some economically depressed or low-cost-of-living areas. I am only sharing what I know for truth in terms of the income of these primary care clinics in NY/NJ area.