Statistics. There have been rare cases of the incubation period being longer than 21 days, but most people will get sick much sooner. (95th percentile)
There's also a cost-benefit analysis involved here. More transmissible/serious diseases call for a larger margin of safety, while at the same time enforcing a longer quarantine takes a toll on total available infrastructure.
That said, there was a recent PLOS article that suggested that a longer waiting period might be called for: http://currents.plos.org/outbreaks/article/on-the-quarantine...
There's also a cost-benefit analysis involved here. More transmissible/serious diseases call for a larger margin of safety, while at the same time enforcing a longer quarantine takes a toll on total available infrastructure.