Earlier quoted context omitted.
Sustaining the infrastructure and support to maintain electronic medical records is probably the biggest. There are so many problems with the current systems that it's hard to know where to start. But related to the context of the article: You can't spread that cost out as a stand alone doctor practicing on rural areas. On top of this is added cost of data entry compared to old paper charts, the cost of training staf…
If computerizing a business makes it more expensive and labor intensive, someone's doing something wrong.
The electronic systems aren't simply recording what the doctor does and making a record of it, as charting is supposed to accomplish. The software is dictating (or at least heavily influencing) the behavior and workflow of the doctor. And anytime something is done out of order results in interrupting that workflow, searching through 10 other screens to find the appropriate checkbox, and then trying to return to your train of thought. The focus ends up being on the data entry instead of the patient.
This is amplified the less specialized the practice is, hence emergency medicine, family practice, and general practice being the most affected. And rural doctors being affected the most since: 1) they generally are expected to handle whatever gets thrown at them since there are no specialists around and 2) they have the smallest practices (can't share costs with other doctors).
Opting out of the system essentially means going cash only, which obviously limits your patients, among other drawbacks. Which leaves burn-out and early retirement or joining a bigger practice in the city. Or concierge medicine, which is one reason why it's becoming more popular.