Reported issue of not being able to access a file in Drupal6 was due to the .htaccess file preventing access to files of that name (in this case a file name prefix sometimes associated with Subversion).
Easily fixed, but got me wondering how it could have been avoided.
There are several issues. Protecting me from subversion when it isn't in use is rather keen, but I don't mind a little mollycoddling.
However the underlying issue is, I think, treating uploaded files like files which are part of Drupal. Of course subversion could be being used to revision the uploaded files whereever they exist in the file system and it might be a bad idea to serve the revision controlled files associated with them.
Various mechanisms could be used to treat the files as a distinct type of thing from the Drupal application files, but probably for most people storing the files in the database would be perfectly fine, then they would receive similar protection, back-up, (replication?) and handling as other user content in Drupal. Of course someone somewhere will be distributing DVD images using Drupal and think this suggestion nuts.
Being Drupal there is already a module for doing this (dbfm), you just needed to know you wanted it that way first. I'm less clear how Drupal 7 handles this (Storage API?).
Microsoft also have some relevant comments on storing files in databases which make similar points, that treating them like other data may result in greater simplicity which may be more important than other concerns.