This directory contains empty CSV files which will be overwritten by PostgreSQL when the data is pulled out of the database and into GTFS format. For multiple agencies, you will likely want to make a copy of this folder for each agency. To finish the GTFS data, you'll need to compress all the CSV files from one folder into a .zip archive.
Note that PostgreSQL needs permission to access these files. If you're having any issues check the file permissions where you're trying to write the output.