We've all heard it a million times. Never get an animal from a pet store because the animal you are adopting is most likely a product of a puppy mill. Puppy mills are notorious for their cruelty and neglect towards their animals. Animals are often housed in tiny cages with sharp wiring on the bottom which leads to injured paw pads. Many have even been known not to provide their animals with proper food or water and many animals are often left to starve to death. It is a horrific living condition for these sweet creatures. It is a business, that's all it is. These animals are used to mass produce animals so the breeder can make a profit. A YouTube video even showed a breeder forcing two rabbits to mate when the female was clearly trying to run away.
On the contrary, it is important to note in the city of Toronto many pet stores have affiliations with local shelters and non-profit organizations like Toronto Cat Rescue. That's not to say that NONE of their animals come from such breeding facilities. However, it's still a step in the right direction.
Many pet stores will host as a temporary location for adoptathons. Furthermore, some pet shops have affiliations with local shelters. They transport the animals from the shelter to the pet store to give the animal more exposure. There ARE reputable breeders out there who treat their animals with love and care.
However, it is simply a matter of doing your homework. Although you may feel you are doing a good thing by taking a pet home, keep in mind it could have a dirty little secret.