The major disadvantage to manufacturing in space is cost.  Currently all space  bound vehicles are government owned.  Fee structures for sending materials into space are exorbitant and delivery service is both uncertain and infrequent.  

It costs approximately $20,000.00 per pound to send materials into space currently.  Although NASA's goal is to get the cost down to $100.00 per pound it is not likely that this will happen any time soon.

Scheduling also remains a problem.  The current shuttle fleet flies about 7 missions per year compared to a goal of once per week.  

Until NASA can decrease costs and increase performance, it is unlikely that anything but research will be performed in the area of microgravity manufacturing.