Unfortunately, breeding isn't always done responsibly and sometimes even when people think they're breeding for the sake of the animal, it's possible to cause negative or harmful traits to pop up. As others have pointed out, some problems may even arise from trying to fix others. Dog breeding seems to be more plagued by poor breeding choices than many other animals, or at least it has been in the past at times - there seem to be more breed-specific "common ailments" in dogs than most animals (like hip dysplasia in some breeds). You don't hear about cats having nearly as many genetic issues as dogs, despite them being just as common for people to have as pets.
While it's hard to argue with the pictures on that website, the site seems focused on being inflammatory - it doesn't address *when* in the last 100 years negative changes became prevalent or whether the breeding community is working to undo any of them. Traits that were specifically bred for even just 5-10 years ago may now have been exaggerated enough to show that they can be harmful and breeders may be moving away from them or trying to un-exaggerate them somewhat to produce healthier dogs... but we don't know if that's the case because the article doesn't explore that possibility - it simply points fingers.
Rabbit breeding is less popularized/mainstream than dog breeding and rabbits were domesticated much more recently (in the big scheme of things) than dogs, which I suspect lends itself to creating a more responsible breeding community overall. The issues that have arisen in the dog breeding world have really come to light in the last couple decades and serve as a warning to breeders of other species, who have the opportunity to learn from those mistakes. Just because dog breeders have made choices in the past that are now widely criticized doesn't mean they'll continue down that path, nor does it mean rabbits will fall prey to the same issues.
One also has to consider backyard breeders and the internet in all of this, given that the article is judging 100 years of dog breeding (keep in mind that backyard breeders can produce "purebred" offspring by starting with purebreds - what makes them "backyard breeders" is a failure to be appropriately selective in pairing animals to breed in order to get the best possible genetics passed to future generations).
The internet only reached the point of being commonly found in the average American home within my own lifetime (I turn 30 in a couple weeks) - I've personally witnessed it growing from something more people than not didn't have at home to being something virtually EVERYONE has; from not really having that much to offer to beginning/intermediate users (ie home users) to practically putting the entire world at your fingertips.
The evolution of online communities and user-friendly public databases changes the face of breeding SO much. A mere fifteen years or so ago, search engines were fickle as could be - you had to carefully construct an intelligent query using syntax that the search engine knew what to do with. If you typed a question into a search engine the way you'd ask it to another human, the search engine would look at you like you were a freaking moron and give you unusable (or no) results. Now, you can literally type in a question and get a buttload of viable results. The internet offers an immeasurable number of online communities spanning nearly every interest under the sun and they're ridiculously easy to find. Information is SO easy to share, exchange and access.
Why does this matter? Because the evolution of the internet has created a widely-known stigma around "backyard breeding" for all variety of animals. I've participated in rabbit, glider and hamster forums (two each for gliders and hamsters) and not ONE of those communities will hesitate to call people out for irresponsible breeding. Does that stop people from doing it? No, but it certainly deters some of them. Communities and resources online also strive to educate those who are planning to get a certain animal on how to find a reputable breeder if they go through a breeder, putting a dent in the potential business available to backyard breeders. It's easier for good breeders to find other good breeders and avoid those who are backyard or mill breeders in disguise (since you've gotta get new breeding animals from other breeders and often sell your own offspring to other breeders). I don't know about the rest of you, but I don't believe for a second that mill breeders aren't responsible for contributing (significantly) to genetic issues in dogs - after all, the term originated from the phrase "puppy mills".
Point being, breeding communities as a whole now have the means to police themselves a hell of a lot better than they did just 10-20 years ago.
Add to that the ability to view and contribute pedigrees and lineages online with a few clicks - responsible breeders can now share information much more easily in the past. If a genetic problem appears in a line, it could affect dozens or more breeders who have breeding stock from that line - databases and communities make being able to inform someone that their animals could be carriers for something easier than ever, helping responsible breeders to weed out harmful recessive genes that they otherwise may never have known they were creating carriers for.
All of that combined makes it fairly unlikely that rabbits will go down the same path.
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Also, even the worst breeding history can be redeemed. Sugar gliders are so "new" to the pet world that they aren't even considered truly domesticated yet. All breeding stock originates from wild-caught gliders, the vast majority of which are standard grays - the "colored" gliders (mosaic, white face blonde, ring-tail, leucistic, cremeino and albino gliders) can all be traced back to no more than 1-3 pairs of gliders who first produced the coloring (recessive traits only) or wild-caught gliders who displayed the coloring.
Because there was so little breeding stock to work with and people had no idea at first how the gene(s) for a color were passed to offspring, those who owned the gliders who started each of the colored lines inbred a disturbing amount in order to reproduce the colorings and figure out the genetic aspects. The inbreeding led to health issues arising - most notably, the "sterile line" mosaics.
Of the three mosaic lines (each line tracing back to one of the three origin points for that coloring), one is considered borderline "untouchable" by some breeders. The sterility issue in that mosaic line is/was x-linked recessive. A female with one "defective" copy of the gene would not be sterile (because it's recessive) but would be a carrier... giving her female offspring a 50% chance of being carriers and her male offspring a 50% chance of being sterile. Because a male who carries the gene is unable to reproduce, it's impossible for a female to get two copies of the gene and therefore be sterile (since one copy would have to come from dad for that to happen).
Some breeders have continued to work with the sterile line mosaics, breeding it out to eliminate the sterility gene (for example, by pairing fertile males from the sterile line (ie proven non-carriers) to females who are NOT from that line and therefore shouldn't be carriers for the sterility gene). After a few generations of breeding pairs who never produced any sterile males, some people consider any future generations in that line to be far enough removed from the sterility issues to make it "safe" to breed them; others are extremely wary of the stigma around that line and are concerned that even though the trait appears to have been bred out, it could reappear in the future.
Even the colored lines that were unaffected by the sterility gene and didn't have any other prominent genetic issues still ended up with extremely high COIs (coefficients of inbreeding) - the higher a glider's COI, the higher the probability is that they're carriers for an unseen/unknown genetic issue resulting from inbreeding.
At this point, an extremely high emphasis is placed on never breeding gliders who don't have lineage (though of course you can never put a complete stop to "backyard breeders" ><) and making very careful choices when assembling breeding pairs by looking at the parents' pedigrees (to see how far back in their history inbreeding occurred, among other things), doing a "test" pedigree for a potential pair's offspring/calculating the offspring's COI and comparing the potential parents on a kinship chart (using their most recent common ancestor if there is one, which there almost always is). Colored gliders where the color is recessive are routinely "outbred" to produce "hets" (short for "heterozygous" and used to indicate that a glider is a carrier or potential carrier for a trait) who are bred to either other hets for the same color or to actual colored gliders in order to produce colored gliders. This brings fresh genetics into a line and dilutes any inbreeding, line-breeding or distant line-breeding that has happened in the past. The kind of inbreeding that happened in the early days of gliders would NEVER be tolerated by today's breeding community and we've made a ton of progress towards undoing the damage.
Responsible for a kick-starting the overhaul is the very breeder I've obtained all but my very first (pet only) pair of gliders from. The primary culprit of out-of-control inbreeding was a breeder named Helen Moreno; when she retired, the vast majority of her sugar gliders as well as whatever breeding records she might've had at that point were passed on to Priscilla Price. It's suspected that Helen didn't even keep much in the way of records, at least regarding glider breeding, or that if she did they were never released or passed on due to the shameful amount of inbreeding they would've revealed... however, the official story given to the community was that most of the records were - and I quote - "eaten by prairie dogs" (which she also bred).
Priscilla inherited the clusterf*ck created by Helen Moreno and sorted it out. At some point, she teamed up with Debby Mountjoy (who I've worked with a ton; I've only had a few conversations with Priscilla and haven't actually met her yet) to form TPG (The Pet Glider). TPG is responsible for creating, hosting and maintaining the primary database of glider pedigrees in the US, allowing breeders to share lineage on gliders and making it easy to spot many irresponsible breeders (because it's so easy now to provide lineage for your gliders that people are instantly suspicious of anyone who can't produce it); the database also calculates the COI for every pedigree and allows you to create a test pedigree for potential offspring which includes their COI.
My point is that it's a complicated process. There is no doubt that selectively breeding domestic animals can better adapt them for the work they're doing or the environment they live in. In some cases, has it gone too far? That is possible too.
