I admire ChuckO's courage. I wouldn't want a glass box sitting in my workshop while I was working on something. Glass sheets, in my vicinity at any rate, have a mystical, almost magnetic attraction; they attract hard objects. I suspect I wouldn't be able to get through the building of a model without busting the glass at least once. My preference is to either build the case last, or build it earlier and keep it far, far out of the way till the model's ready to go in it. And I generally prefer plexiglas to glass. (That's another issue.)
My inclination is to keep the in-progess model in a cardboard or foamboard box, if necessary custom-making the box to fit it. I tend to spend a long time on my models; the biggest function of the box is to keep them from gathering dust (sawdust and other) during the long periods when I'm not working on them. I like to screw the model down to a baseboard early in the construction process, and make the box in such a way that the baseboard gets fastened firmly to the bottom of the box.
When I was in the early stages of my little Continental frigate Hancock (which is shown in my avatar), somebody bashed into the rear end of my 1978 Chevy Monza and punched out one of the tail lights. The replacement tail light assembly came in a nice, sturdy cardboard box that was a good fit for the model (without masts or bowsprit). I glued a couple of strips of wood inside the sides of the box, so the baseboard slid between them and the bottom. The model traveled across the Atlantic and back in that box, inside a suitcase, and made it in fine shape. (That model has more miles on it under the American flag than the real ship did.)
One day about three years later, as I was sliding the model into the box again after a work session, I thought to myself that the box was looking a little ratty. Sure enough, that very night, in a rainstorm in Newport News, Virginia, I stopped at a traffic light and got rear-ended by a Toyota, which punched out the other tail light. So (courtesy of the driver of the other car - which was totalled) I got a nice, new box. The model lived in it till I installed the bowsprit, at which time I had to make a new box for it.
I can't think of a practical way to protect a sailing ship model while it's actually being worked on. If the model is really large, and if you have a big enough shop, it might be worth considering setting it on a purpose-built table in the middle of the room and walking around it. Most of us don't have room to do that. If the model has to be turned around, unfortunately, there's always going to be a possibility of bumping it into something.