As a bag guy at the moment, I'm going to have to agree with Kristie. I've seen guys who wouldn't care less if they chucked a fragile bag halfway across the ramp take a cat/dog/ferret and personally walk up the belt loader to set it down carefully and slowly in the bin. That's not to say everyone does it, but most people, regardless of normall carelessness levels, tend to be very careful with animals.
My warning lies in a completely different area, though. Despite the employee care, the animal is going to be put through a lot and without its normal comfort zone around it (comforting people/environment/etc). First, it's in a cage it normally isn't in (in many cases anyway). Second, it's in bag carts driven by idiots. Third, it's out on a ridiculously loud ramp, which is even louder when you have very sensitive ears. Fourth, at this time of year it is very hot. Airline rules generally specify a certain time period where the animal is fed and given water (mostly 12 and 24 hour periods), regardless of outside temperatures. If there's no connection, it's just fine, but with the connections, it can be taxing on the animal.
Those are just my warnings. Every time I've seen an animal, it has been well cared for even by the worst of the employees. The problem is just the chaos and atmosphere of the airport, however. If her dog is strong-willed and okay in strange situations, it shouldn't be too bad.