Layers are useful for trying out alternate layouts of objects when you're building a route.
For example, say I'm getting ready to place an industry by the tracks. In my mind I can think of two ways to place the various buildings, etc.
I'll make two layers, one titled "version 1" the other "version 2".
I select the "version1" layer and place the various objects that make up the industry. I then hide the "version 1" layer, select "version 2" layer and do the alternate layout.
I can then switch back and forth between the two versions to evaluate what each looks like. If I decide that version 2 looks the best, I just delete version1 and merge version 2 into the route layer.
Without layers you'd have to place all your buildings, then delete them all then do the alternate layout. Then, if you decide the first layout looked better, you'd have to delete everything again and re-do the first set of buildings.
This is a big timesaver as some industries are quite complex with multiple buildings, fences, parking lots, etc. And many times those objects have to be placed precisely in relation to each other and lots of time is spent tweaking their positions.
Todd