The list of differences is long, however THE most important thing is the wood. Not just the types of woods (yes, different woods for different parts) but also where did the wood come from (trees that grow in colder climates grow slower so growth rings are tighter), Once a piece of wood is cut, it needs to air dry for a minimum of 20 years (the wood for many high quality instrument dries for 50), how the wood blank was cut (when cut properly there is a lot of waist, most factories simply cut as many as they can get out of a blank). Once you have the proper wood, cut correctly and dried the right way and for the proper amount of time, then a master crafts person can start working with the wood and that opens a whole new set of issues. As you can see from just talking about wood to get started, its time consuming and expensive process. That theme is present in every step.
I hope this gives you some small idea of why quality instruments cost so much more than ones made in a factory.