In theory, to prevent a conflict of interest. Please note the key word is theory. The theory falls apart when you dissect it. In practice, it is whoever has the best lobbyists.
The idea going back to the early 20th century was that there would be a conflict between the physician's duty to act in the best interest of the patient, and the employee's duty to act in the best financial interest of his employer. This is also linked with, and the rational behind, the fact that the "corporate practice of medicine" is illegal in most states. Emergency medicine, pathology, radiology and anesthesiology are singled out in some places for special restrictions because their practice of medicine is almost exclusively within the hospital. A family physician, for example, might have a practice that is owned by the hospital, however, there is not a complete overlap with what he does and the hospital's operations. (Think of those Venn diagrams from high school.) On the other hand, basically every decision the EM physician makes directly effects the hospital's profit.
Also, a hospital has more power over "hospital-based specialties" than they do over other physicians. Lets say a family physician is affiliated with a hospital and he thinks they are behaving unethically. It is far easier for him to break away from the hospital and continue his practice than it would be for an EM physician or an anesthesiologist. No hospital, no job. For these specialties, the hospital holds all the power - at least traditionally they have. It is far more difficult for a hospital to cancel an entire contract rather than fire an individual physician. This, theoretically, means that EM physicians have more freedom to make decisions in the best interest of the patient.