Global Limo Inc. and its president and director, James H. Maples, are accused in a three-count federal indictment of conspiring to falsify driver time records and failing to inspect buses to ensure their safety.
Maples, 65, didn't comment as he left the courtroom. His attorney, Charles Banker III, has said the government was blaming Maples for "something that was really completely out of his control." Maples was arrested Wednesday and released on a $75,000 bond.
The bus erupted into flames Sept. 23 on a freeway near Dallas while carrying evacuees from a Houston nursing home as Rita gathered strength in the Gulf of Mexico. The driver and some passengers escaped, but others were caught inside as patients' oxygen tanks exploded.
The accident accounted for almost one-fourth of the approximately 100 deaths linked to Hurricane Rita.
Federal regulators shut down Global Limo's bus operations after the fire, saying the conditions of its vehicles and drivers "are likely to result in serious injury or death." A grand jury declined to indict the driver.
Prosecutors said the violations in the indictment are not necessarily what caused the accident, which remains under investigation by the National Transportation Safety Board.
"We can, when laws have been violated, hold people accountable to the laws that have been violated," federal prosecutor Don DeGabrielle said when the indictment was announced last week.
The conspiracy charge, the most serious, carries up to five years in prison and a $250,000 fine. If the company is convicted on that charge, it could be fined $500,000.
U.S. Magistrate Judge Dorina Ramos scheduled jury selection for early April.