According to Marc Thiessen it's because in 2001 - 2002 (when the key decisions were made on what to do with Reid) we didn't know we had other options like military tribunals. (Now that's obviously false since extra-judicial means were amply discussed from late 2001 through early 2003 -- when we decided how to deal with Reid). The proof, says Thiessen, is how we dealt with Jose Padilla, who was transferred to military custody in Charleston, South Carolina.
But again, that's clearly preposterous.
The reason we handled Padilla that way was because we didn't have clear evidence to try him in a civilian court. If that were the case why did we try all the other people arrested in terrorist plots after Padilla in civilian courts? It can't be because they were American citizens, because Padilla is an American citizen too.
There's no way to spin this. There's no reason beside GOP electoral strategy for not trying AbdulMutallab in a regular American Court.