James Polehinke, the flight's co-pilot, can move only his head, and tears often well up in his eyes, said Antonio Cruz, Polehinke's mother's boyfriend. He said the 44-year-old has been in and out of consciousness.
Polehinke has not mentioned the crash, and doctors have encouraged family members not to ask him about it, Cruz told The Associated Press.
According to federal investigators, Polehinke was controlling Comair Flight 5191 when the regional jet took off from a too-short runway at Lexington's Blue Grass Airport, crashed and caught fire in a nearby field on Aug. 27. He was pulled to safety from the broken cockpit, but everyone else aboard the plane died in the crash and fire.
Polehinke is now off a ventilator, but could be hospitalized for several more weeks with facial and spine fractures, a broken leg, foot and hand, three broken ribs, a broken breastbone and a collapsed lung.
He has asked about various family members and his dogs, Cruz said, and has questioned his relationship with God.
One of the first full sentences he said after regaining consciousness was, "Why did God do this to me?" Cruz said.
Cruz said Polehinke's mother, Honey Jackson, told him: "It was not God. It was just an accident."
Investigators are looking into airport construction and staffing at the control tower, among other things, as a possible contributing factors to the crash. The lone tower operator had turned to do administrative work as the plane turned onto the wrong runway and tried to take off, officials said. According to FAA guidelines, two control tower operators should have been working at the time.