Personally i feel using a database much easier to delete, update and display data as well as it being much faster. Flatfiles are great if you have little data but once they become big and cumbersome they very slow loading and take a long time to change data.
However if you wish to use flatfiles. Why not use them outside the WWW Document Root.
E.g.
/home/username/public_html (public_html is the WWW DocumentRoot)
Placing the files in the username in this example is outside the WWW DocumentRoot.
Accessing the files. You must do it directly e.g.
/home/username/test.txt