Trevor hit it on the nose. Back in the fifty's Walt actually had a taxidermist on staff, the animals you see are real and would fall apart due to real weather getting in that tunnel. Also to protect that giant mural that is one stretched piece of canvas (one of the largest in the world)!!! As a conductor it is our job to spiel about not using flash, doesn't seem to do any good though as there are many flashes every trip...
Wow...I wonder where they got all those dinosaurs to stuff?
Everyone has mentioned the reasons...inconsiderate guests, grime, etc. It's simply a lot easier to clean the glass every day than it would be to crawl into the dioramas every night to retrieve the assorted junk people would throw, clean off the food stains, etc.
It is possible to take nice pictures without a flash. Just need patience and the right lens.
I never use a flash and my camera is a Fuji Fine Pix camera and it turns out pretty decent looking pictures for a cheap camera (what are they? $80?). Just look at my Youtube slideshows. Less than .10% of those pics were taken with flash. Some photos, especially from the 2010 trip, were taken on the photo setting of my cheapo Kodak for cheapskate flip style video camera and it has no flash whatsoever and still, you can get some decent photos.
To be honest, my first thougt wasn't of the littering guests, but just the general dirt from the steam, and dirt blown up everytime a train goes through. That would probably cause more damage than litter from inconciderate guests.
The dioramas are like the ones at the Natural History museums really--the glass is there to protect the scenes from both train passengers and to control the environment (remember, the animals are stuffed). Without the glass, the stuffed animals would not have survived nearly as long.