RE: Tons of questions...
I ship puppies and dogs all over North America. I've also received shipments of my own dogs and pups. None of them end up "skittish" as a result of the flight. I could supply you with dozens of references from people who have gotten their pups this way...and all of them will tell you the pups are fine, bold and friendly on arrival.
Don't blame the process...it works just fine. Blame the dog's breeding/breeder if you must, or, perhaps place blame on yourself for not handling the pup correctly after receiving it.
As far as an eye infection that has progressed, all puppies must have a state-certified health certificate issued by a vet within 10 days of the flight. If a vet let that puppy fly with an eye infection like that, I'd turn him or her in to their state board. The vet's signature must be on the certificate...so tracking the offender down should be no problem.