There are rules in place, based on how the hijackers or planners are viewed, the dictate whether a civilian or military court is called for. If the planners of 9/11 were civilians acting as such, civilian courts are needed; if they're enemy combatants, 9/11 was an act of war, and a military trial is needed.
Military detainees should be tried in military court because it has different rules and guidelines and is better prepared to handle the extenuating circumstances specific to 9/11. Trying these individuals in civilian courts would be cumbersome and tie up the court system which is already overloaded. Military counsel has more experience in this area and available resources which would be difficult to provide in civilian court.