For an upcoming mod I need a drivable vehicle that can "fly", but thrusters on a physbox aren't doing anything--the player falls right through it, and it doesn't move.

Is there something big I'm missing?

For the model I used "prisoner_pod.mdl" from Half Life 2, and the script
"choreo_vehicle_ep1_dogintro.txt" in the ..\scripts\vehicles\ folder.

You can change the clamp angles at the bottom of the script, and trigger enter\exit via something like
ent_fire vehicle unlock
ent_fire vehicle entervehicle
ent_fire vehicle lock
ent_fire vehicle exitvehicle

Etc.
Bear in mind though (rawwwr) that there's no camera smoothing when the vehicle's parented to your cube or anything, so movement entirely via vscript (10 frames/sec tops) would be insanely jumpy.

Hope that helps