To re-phrase Richard's quote in simpler terms, the replicator is the end stage of 3D printing. It works by creating a form and filling the form with material. So, for example, if you want a glass of water the instructions will read like this:
create a cylinder 8cm x 12cm, 5mm thick, one end closed. 50% radius on all corners. Fill with glass at 20 degrees C. Present closed end down.
glass: SiO2, amorphous form.
create 400ml water (H20) at 5 degrees C. Put in cylinder.
It took me 2 minutes to write precise instructions to create a glass of water out of bare elements. Now picture the instructions needed to create a mouse. Sure, you can create arrays for things like hair, and bones are often mirror copies, but working organs are a different matter. Not even Star Trek computers have enough memory to keep that on file.
The transporter just moves you from place to place - it doesn't save a full specification.
If it did, we could have this scenario