There are as many potential reasons to avoid the surface of a planet as we have hours to sit around and brainstorm them, so I'll just offer what I view as the most proximally-likely scenario and count on the community to contribute to the diversity of answers.
Autonomous Drone Warfare
When every dot on the horizon that might be a seagull might also be an autonomous drone bringing a payload of missiles to your address, that provides ample motivation to make yourself and indeed your entire community invisible (or at least inaccessible) from the sky. The thing about emerging technologies is it can be difficult to control access to them. The drones on the horizon might belong to your government (which may or may not make you feel safe), another government (which probably wouldn't), or just any damn kid with a 3D printer and a set of schematics they downloaded from some edgy website. Americans in particular like to kill as many people as they can manage every once in a while, whether because the CIA brainwashed them or a girl rejected them. Imagine James Holmes with a dozen armed drones. Yeah, let's just live underground, now.
One other point... You seem very attached to the idea of access to natural light, but so long as there are alternative energy sources available (nuclear and geothermal spring to mind) it's not strictly necessary. Thanks in large part to the efforts of the US Drug Enforcement Agency (or rather, to citizens' efforts to counter that institution), growing plants without natural light isn't even a rich man's game: it can be accomplished surprisingly cheaply, easily, and with a minimum of energy input thanks to the advent of LEDs that produce just about any wavelength of light you'd like (LEDs that produce agriculturally-appropriate wavelengths are very commonly manufactured and benefit from the economy of scale.)