Of course they are... but some breeds are more screwed up than others.
We've bred dogs to do certain tasks in life. And it shows in their form and confirmation. It isn't necessarily a bad thing to start with, but people got all into inbreeding and didn't know about certain bad traits, recessive genes, etc, etc, blah blah blah. (Like Quarter Horses with HYPP from one sire, named Impressive. He was so pretty and wonderful that they bred him to every Quarter Horse out there, now most Quarter Horses have this really bad disease. They just didn't know.)
It also happens when a dog breed becomes "popular" and all of a sudden, it's hard to find quality dogs of that breed, because everyone with a ghetto lab will breed it to another ghetto lab and suddenly you have rampant hip dysplasia, dwafism, skin disease, etc, etc, above and beyond what is the "norm" for the breed. Same with Rotts, Pits, Chows, and every other popular breed. A good thing gone bad.
However, some dogs just weren't meant to be. All of the chondrodysplastic breeds and brachycephalic breeds, IMO. :P We just need to get them out of the population. Sure, you like some of the things that go with the particular breed. Pugs for instance, are exceptionally sweet dogs! Great for kids. Of course, there's the whole brachycephalic airway syndrome, pug encephalitis, mouth disease, eye problems... if you want to retain the good pug traits, but get rid of the bad pug traits, just start breeding it out of them! :P
But.. that'll never happen. Gotta keep the pet stores full! Go Go Puppy Mill Power! :P
And if nothing else, all the wienie-dogs with back problems and pugs and other squished faced dogs with airway problems, and Boston Terriers and Bulldogs needing C-sections will keep me in business for life. :P