Answers:
Slate's Daniel Engber dates the modern usage to 1974 college campuses, where it was perhaps an outgrowth of the Vietnam War . The origins of the phrase are uncertain, with some speculating that it may refer to being "out in the open" or "ready for action." According to Engber many soldiers do go without underwear to "increase ventilation and reduce moisture." The earliest known use of the term in print is January 22, 1985 when Jim Spencer wrote in the Chicago Tribune:
Furthermore, colored briefs are 'sleazy' and going without underwear ('going commando', as they say on campus) is simply gross".
"Going commando" may also come from the mistaken idea that "commandos" go into an area "without cover."