Given the amount of money needed to keep the Big Three automakers afloat, it's a lot more efficient to simply lend them the money rather than to spur sales through an incentive program.
American consumers also don't like to be told what to buy. A rebate program would have to specify that they purchase a vehicle from General Motors, Ford or Chrysler, limiting their choices to the Big Three. Consumers and foreign-based manufacturers would likely pressure the program to open up to at least all cars made in the United States.
Also keep in mind that the government isn't giving money to the automakers - it's lending it to them, with the intention of getting it back in a few years. Rebates are not loans, and consumers could not be expected to pay them back.