Dominic, I have an Atlas GP9 and a F3. I don't consider them fragile, but I have broken off one of the handrail stanchion mounts on the GP9 (due to my clumsiness).
I have quite a few Atlas freight cars and the only one that has broken was the 1st car, a red Swift Reefer (broke one of the stirrup steps within a couple of weeks of getting it).
It could be that, given the price of their stuff, I handle them a bit more gently, but I've also noticed some of the handgrabs and such are made of metal on later models.
The area I would be concerned with when handling their freight cars is the underframe detail, I always seem to grab onto something that wants to move/bend when I touch it but I haven't broken any of it yet. I do handle my freight cars more frequently than my engines.
As many times as I've had the GP9 apart and only broken 1 stanchion is proof to me that they're built fairly well. It started out as a dummy unit, then got PS2. A week or so ago I wanted to cut a hole in the chassis for the battery charging jack so had to take it aprat again. While I had it apart I took out some of the wiring that was not being used, to free up some space inside the narrow, scale body.
I would handle it just like any on $600 item I have around the house that I wanted to keep problem free.