I had a hard time understanding how this could be true, until I read the simple math example presented. The problem seems to be one of externalities. Each individual driver is selfishly optimizing for his own travel time, but by choosing to drive in a short-congested route, instead of a longer-sparse route, he's negatively impacting the travel times of everyone else around him.
It's been well proven in economics that externalities, if unregulated, will produce sub-optimal outcomes. That the way to restore optimal outcomes is to impose a tax that's proportional to the negative externality imposed on others. In an ideal high-tech world, this can be achieved by having differential prices that each driver has to pay, to use each road/highway. In a low tech world, narrowing/closing a road is akin to imposing a tax on certain routes, which explains why it can counter-intuitively help us get to a more optimal outcome.