Truthfully, I agree with everything Luisa mentioned in her article.
Show breeders are mentioned the most because in many working breeds (such as the border collie), they're glorified for producing the prettiest dogs that are in the spotlight the most. When truthfully, they are a variation of BYBs. I do not mean this to be offensive to the members here who breed their dogs for the show ring - chances are, your breed is not widely used to do what they were originally bred to do. I don't know many Beagles who are still needed to hunt in packs, or GSDs that are needed to tend flocks, APBTs that are used to fight other dogs, etc. Border Collies are still needed as working dogs, and to breed for anything other than working ability is to harm the working Border Collie as a breed. If someday there are no more sheep or cattle farms and people don't need herding dogs, then by all means it's doing right by the breed to select for other traits. But until then, breeding away from the original purpose (the "standard", I guess you could say) is only hurting the breed.
Breeding show dogs from show dogs? Fine. I have 2 dogs from show/sport lines and it's very clear that they were bred as show/sport dogs, FROM show/sport dogs. In most of the breeds that still fill their original niche, you have a very sharp, distinct line drawn between show lines and working lines. It's almost like they are two separate breeds. If you keep to those "variations" and don't harbor illusions about the working ability of the show-bred dogs, I see no problem with it. Just don't take existing working lines and ruin them for work by breeding for appearance only. People buy dogs from working lines because they want a dog that can do it all, but why is it so important that a dog win a conformation championship? If it's of major importance to anyone, they're not breeding for a working dog, they're breeding for a pretty dog that can also work. And soon the pretty side takes over, and the "work" standard gets lower and lower. What does it matter, anyway, since the dogs are "just pets" most of the time? This is the kind of thinking that sends the quality of a former working breed down the gutter.
As for the instinct being present in all dogs, that's halfway true. Yes, a skeleton of the "herding instinct" remains in dogs no matter how far removed they are from their heritage. My show/sport bred dogs still have an interest in stock, they'll still pursue livestock and try to stop them, but is that herding instinct or prey drive? Is nipping at a running child's heels indicative of an ability to control livestock, or is it the little voice that every dog has in his head, saying "chase things that run away"?
The term "instinct" is thrown around way too casually. Look at Bev Lambert's dog working in that video clip. The ability to control sheep at that level of precision at that distance? THAT is herding instinct. Yes, Pippa has been highly trained but training can only take a dog so far. She has natural working ability. No matter how much I train Dakota, he will never be able to do that. He doesn't have the inborn ability.
Show breeders like to kid themselves and think that their dogs can do exactly what Pippa does in that video. THEY CANNOT. If they could, AKC's herding trials would be the same as the USBCHA herding trials. AKC trials would have a 500+ yard outrun in an open field, not a 20 yard outrun in an arena, if the working ability was the same. AKC trials would have a shedding activity, a long fetch and drive, sometimes a double lift outrun (I know it's a lot of lingo, and I don't have the time to define it all. Suffice it to say, these things are not easy.) But the working ability isn't the same, and it's unfair to expect a show dog to be able to work at a high level, just as it's unfair to expect a working-bred dog to win best in show at Westminster.
I ramble. I always ramble on this subject. So, in short, I agree 100% with the author of the blog. I think she's one smart gal.