I guess my overall question is why is it such Taboo for people to have BYB dogs?
I'm not saying this to be catty but you've posted in two threads now that explain the horrors that BYB's cause and you've also been linked to a couple of threads about it. In all of these threads many people have shared their experiences and given their opinions.
My question is, has it not been explained in a way that makes any sense to you?
To answer your question...
BYB's and Greeders are doing nothing but produce puppies. They are taking members of a breed and breeding them without health testing them (or doing minimal tests) nor titling them. They are doing nothing to check the health and ability of their dogs, they're just throwing caution to the wind and creating puppies - almost certainly for nothing but profit.
"Reputable" breeders on the other hand are actively titling their dogs to prove them. TO prove that the dogs are built correctly (a dog that is not built correctly will deteriorate faster than a dog that is) and/or that they can work under pressure. They are also fully health testing all of their dogs before breeding them to make sure that they are only breeding healthy dogs.
What it comes down to here is that you get the unknown from the unknown (dogs that aren't tested or titled) and you get MUCH better chances at health, correct build, correct temperament, etc from dogs that have been tested for all of those things.
Also, "reputable" breeders screen their buyers heavily - and sure, I can see how some people get offended by this but it's all in the best interest of the dog (imo). They make sure that their dogs are going to the best homes possible, homes that are prepared, so that there is little chance of the dog ever leaving that home. However, if, for some reason, those dogs do have to leave the original home the "reputable" breeders will take those dogs back to ensure that those dogs never set foot in a shelter or rescue nor in the hands of somebody that they don't know anything about. These breeders keep a close relationship with their puppy buyers.
On the other hand, BYBs and greeders will sell their dogs wither with minimal screening or to the first person with the money. After that transaction they are done with the puppy and pay no mind with where it ends up or even if the buyer should have one in the first place. They are not breeding to improve the breed - simply for reasons such as money. They are populating the world with far too many dogs and it's THEIR dogs that end up filling up shelters.
ETA: There are many BYBs and greeders who are just really nice people. They come in all shapes and sizes, they sometimes are very open about their religion and sometimes aren't; They are people.
However, just because they're a friendly person doesn't mean that they should be breeding dogs.
And yes, as somebody stated, the taboo isn't the dogs or having the dogs - it's knowingly supporting the practice.