After Directive 10-289 went into effect, there were a large number of people who simply couldn't stand living under the circumstances created by the directive anymore and simply vanished. Most of them don't appear to have joined the Strike; at a minimum, when Dagny went to the Valley, Pat Logan (engineer of the Comet, and engineer on the first freight train on the John Galt Line) was apparently not there (even though on the face of it he seems like he'd be an excellent candidate for joining the Strike). Where exactly were they going, and how did they survive? Are there any clues in the book as to their ultimate fate?
I can make an educated guess based on a few clues left in the book. Consider the following passage:
There were whispered rumors of covered wagons traveling by night through abandoned trails, and of secret settlements armed to resist the attacks of those whom they called the "Indians"—the attacks of any looting savages, be they homeless mobs or government agents. Lights were seen, once in a while, on the distant horizon of a prairie, in the hills, on the ledges of mountains, where no buildings had been known to exist. But no soldiers could be persuaded to investigate the sources of those lights.
Those who were not Strikers and not Looters lived as they could, self sufficiently and off the grid. It's reasonable to assume that Pat Logan and others like him lived in one of these secret settlements.