There are many different animal shipping "packages" you can pay for that vary by airline, but regardless, regulations require that they are flown in pressurized and temp controlled areas of the plane. Additionally, airlines cannot fly an animal outside of the main cabin if there are either cold or hot temperature extremes. This is often due, not due to the on flight conditions but the wait while the crates on on the loading carts outside the plan. Many also have limits on brachy breeds.
Here are some examples of how the airlines put the regulations into action and each airline will have similar info: Pet Travel Requirements & Restrictions | Delta Air Lines United Airlines - Travel for animals
I read the blog and she raises some good points, but I still think it's more ideal for buyers to be able to see the premises and meet the animals so they can be sure they aren't supporting puppy mills and bybers.
IF you really trust/know your breeder, I think shipping is fine for many dogs/pups. Of course, I wouldn't recommend flying a pup alone if it is timid/shy. I would also recommend your breeder accustom your pup to a crate before shipping.
If you drive to pick up, it's just common sense not to take the pup onto public areas for breaks--if a buyer is too clueless to know about that, then I'd question whether or not they are ready for a pup anyways. And a breeder concerned about bio-security can easily implement foot bathes, hand washing, scrubs/overshirts, a visitor area, etc.
As far as shipping pups personally, we have had puppies shipped/flown to us, flown out puppies ourselves, had people pick up/drive, and had people pick-up/fly pup as carry on. All of our pups have been fine upon arrival whether with us or their new owners. We plan for phone calls b/w breeder/owner when the pup is checked in and on arrival, and we have phone numbers for the customer service at each location for our airline/cargo service to keep tabs on what is going on.