In fact, most respondents described net income from their practices as "disappointing." Nineteen percent of physicians reported that their income was down by more than 10 percent in 2012, compared to 2011.

Fewer physicians than ever (44 percent) report being owners or partners of their own practices, as hospitals and health systems continue to seek market share through direct employment and practice ownership and smaller group practices consolidate. Almost 44 percent report that their practices are owned by a hospital or health system.

Additionally, 29 percent of physicians say the viability of their business is "shaky," a scary prospect just as more patients are getting access to care.

"Physician compensation is not very well understood by the general public," says Bob Keaveney, editorial director of Physicians Practice. "Compensation for doctors continues to be governed mainly by their specialty and the complexity of the cases they see."

 Almost 40 percent of primary care physicians—and a majority of pediatricians—make less than $150,000 a year. But only 29 percent of OBGYNs and 10 percent of radiologists fall below that threshold.

Keaveney also says there are even more worrying signs on the horizon. If the fiscal cliff issue remains unresolved, there will be a 27 percent cut in Medicare payments to physicians on Jan. 1. Now, 15 percent of practices reported that they are no longer accepting new Medicare patients, but that might change if cuts go through, Keaveney says.

Meanwhile, reductions in Medicare spending contained in the Patient Protection and Affordable Care Act may erode physician compensation, especially for practices that struggle to reap increases in outcome-based payments, the organization says.