In most cases, glasses are only a cast, but then nobody claimed that they are anything more than that.
Off the top of my head, the only time I can think of glasses improving vision is in children with amblyopia, in conjunction with patching. There will actually be a biological/neurological change.

Most body tissues do atrophy without use, but I don't see how having glasses on causes you not to use your eyes. The neurons at the back of your eye are receiving light in both cases, but without glasses if you have a refractive error, the light is not being focuses, so I'd say the eyes are being 'used' less if they're getting out-of-focus images, no? This is in fact what causes kids to develop amblyopia.
Refractive errors where you can use your focusing muscles to overcome it are the minority (hyperopia), and this focusing is supposed to be used to see things up close, so if you are using it to clear things up in the distance, up close will be even harder. This usually leads to headaches, fatigue, and sleepiness with prolonged close work. With refractive myopia, you can't do anything to clear your vision, so not using glasses won't make a difference.