Well there are a number of reasons, the primary reason being is that there is no need for them as any place that supports commercial air transportation has an airport nowadays. So why make a separate model that can't fly inland?
Secondly, if its a seaplane vs flying boat, the floats are not good for aerodynamics. I would suspect on flying boats the design compromises to make it work on the water would bring other issues that would make it difficult to compete with land-based aircraft.
There are definitely smaller operations, for example in the Pacific Northwest that use seaplanes/amphibians for island hopping, and they are used in bush operations in Alaska and northern Canada. I flew on a seaplane out of Lake Union to do an aerial tour of Seattle.