One reason for the inflated chargemaster prices (e.g. $100 for a tylenol) is that payers (Medicare is a big one) simply negotiate by saying "I'll pay you 50% of your chargemaster". Then when the hospital updates their chargemaster, they tack on another 20% and the payer comes back and says "I'll pay you 25% of your chargemaster".
It's a vicious cycle where the chargemaster prices have no bearing on reality.
An insurer last month for a relative's pediatrics practice announced that they were having difficulties with their accounting system and so they would only be making a half payment on their outstanding AR (and naturally, they announced this problem right before the payment was due to be sent). My relative's practice has no practical recourse other than to wait for the full payment to be sent. This is not an uncommon occurrence. My relative's practice is regrettably not able to use the same argument for their bills that are due.
It costs my relative money to administer vaccines in their peds practice, i.e., most insurances pay less than what it costs to purchase and give the vaccine. My relative continues to offer many vaccines at a loss because they believe vaccines are one of medicine's greatest gifts and because they have good success in persuading unsure parents to vaccinate their children. From a pure numbers perspective, it is a mistake.
Insurance companies not paying physicians on time as agreed drives up costs. Insurance (Medicaid included) not paying what it actually costs for a procedure drives up costs. Insurance companies arguing against the best course of treatment for a patient, requiring additional staff to be hired in order to deal with the pushback, drives up costs.
Maybe we need to drop kiosks into pharmacies that can read biometric markers, get doctor approval, and deliver vaccines.
The vaccine itself. Medicare and Medicaid are notorious for this, as they have no mandate to cover marginal costs of supplies (and they have the ability to force providers to accept less than that).
So, depending on the practice, those providers could very well be losing money on every Medicare patient they treat before they even have a chance to think about paying for their office space, paying their staff, etc.
It's a really frustrating thing, as a physician you want to treat everyone, but accepting Medicare and Medicaid can really hurt the operation of your business.
Doctors take home a lot less than people think.
The "salary" numbers you usually see cited aren't comparable to salaries in fields like software engineering, because doctors still have to cover their own business costs (the big one is malpractice insurance, but other expenses like CME, etc. are all on their own dime). And these are almost invariably not tax-deductible, because AMT doesn't allow for deductions for business expenses.
In any case, physicians' earnings account for only about 10% of total medical spending in the country. In other words, even if every doctor decided to work for free and pay for all their business expenses out of their savings... we'd still be spending 90% of what we currently are.