I once asked a veterinarian what breed has the lowest medical costs due to congenital defects, and they said chihuahuas. The reason: anesthesia and medications are dosed by weight. They then went on to list the medical issues each breed is susceptible to. It took a while.
The article explicitly calls out why this research is helpful: because we, as humans, have bred large dogs to die early as a side effect of their size.
It's really hard for me to understand why people are okay paying a dog breeder to perpetuate significant health problems. Plenty of owners are ignorant, but plenty of people fully understand that the Irish Wolfhound that they're going to purchase and grow to love will quite possibly die of old age in seven years, and that paying even a responsible breeder who's trying to minimize this problem will _still_ result in more dogs that die too young purely for our preferences.
I expected working dogs to actually be largely free of genetic issues, which is why I asked -- but somehow we've _still_ managed to give them a bunch of problems.
And that's discounting the fact that most people simply don't have the will or the time to give a working dog the attention and stimulation that it needs to not be a neurotic mess.
Logically applies to the small dogs too - they're still going to die, and they're only here because of our preferences. It's about where you, personally, want to draw that line, and different people have different thresholds.
(Rabbits and fancy goldfish have similar "live pretty, die young" problems. Probably a whole host of other animals - anything we've bred for shortened heads is likely to have breathing problems - including the Chihuahua).
Selecting breeding is what made dogs into creatures useful for people somehow, whether for working (herding etc) or as pets. Without breeding, you just get wild animals unsuited for human companionship.
However, I still agree with you: I think selective breeding of dogs is wrong. If they don't make good companion animals as they are naturally, then maybe people shouldn't try to turn them into such animals.