Except the banks payed it back. The US government profited about $15bn from the bailouts. Potentially a loss if considering inflation. Also banks were forced to take the bailouts to prevent a bank run. You would almost certainly have taken your money out of CITI bank if they were the only ones receiving a bailout from the government. Which would have cost the government more in the long term.
Large banks like JPMorgan and Goldman Sachs had already paid back the government bailout by July 2009.