Cheney vs The Facts counters Cheney's claim that the shoe bomber was not put into military custody "primarily because he plead guilty":

But Reid didn’t plead guilty until Oct. 4, 2002 – nearly 11 months after his arrest. Events suggest the guilty plea was a surprise to prosecutors Reid had been scheduled for trial in November. For nearly a year, then, the Bush administration had the option of transferring Reid into military custody, but didn’t. Then-Attorney General John Ashcroft even discussed the idea with DoD early on, but the decision was made to proceed in the civilian system, according to Ashcroft, who was asked about the possibility at a press conference a little more than a month after Reid’s arrest.