Because enforcing a thousand tiny regulations like, no higher than x decibels, no more than 10 people, and no leaving doors to common areas open is difficult. A short term tenant finds it easier to get a way with breaking these rules because he knows he will be gone tomorrow, and it is more difficult for people to associate him with a particular apartment if he's only been there for a few days. Most cities realized that length of tenancy is a good heuristic, so to make enforcement easier they developed zoning laws around it.

There are real objective difference between living in a building with short term vs long term tenants, and there is no easy way to force short term tenants to behave like long term tenants.