Not necessarily. The military itself is made up of citizens. Plenty of them would desert as they aren't really interested in shooting their friends and family. They would take their skills with them. There are plenty of mountains and desert and other inhospitable terrain with hiding spots where rebels could hole up for long periods of time. Small arms would be handy for random minor engagements with patrols, hunting for food and defending against wildlife. Obviously they're not going to take on tanks and jets with them but they're essential to guerrilla warfare and very helpful in wilderness survival.
Really it would just be a matter of surviving until the lack of supply and support from civilians kicked the military's feet right out from under them.
You make it sound easy. As I said, the taliban and groups like them are extremely highly trained and have been fighting and surviving through war for most of there lives. They are also much more well outfitted then people understand. Guerilla warfare isnt quite as simple as you are implying. Surviving in the wilderness is anything but simple or easy. The "people" would not stand any kind of a chance of fighting off the American military if it were somehow turned against us. Non military Americans have no idea what war is and are extremely soft, comparitively speaking. Less then five percent of Americans serve in the military and even less see real combat.