The question "Is it safe?" is one we hear quite often. We feel it is a very safe and good way to transfer a puppy - if nothing unforseen occurs. We have shipped many many puppies very successfully and likewise we have received quite a few that we have purchased as well. To date we have had only one mishap. Our puppy was supposed to fly into one airport and somehow ended up in the next airport in a nearby town. The people purchasing our pup were very caring and drove the extra hour to go get thier new addition. Things like this can of course happen - but they are very very rare.
In addition to that trouble, we suppose that your pup could come into contact with some uncaring person who could handle their crate rather roughly. However, with the regulation now on the airlines and the public scrutiny they had several years back it appears that the responsible care the live animals now receive is regular practice.
Shipping a puppy is a scary new experience not much different than us putting them in their crates and taking them in our car to the veterinarians office. Every new place, sound and person is frightening to a pup whether it comes from being on a plane in a crate or in your car in a crate. New experiences although scary are all part of the socialization process.