Meh... try if this works:
$ cd ~
$ mkdir .fs2_open
$ cd .fs2_open
$ gedit fs2_open.ini
Or use any text editor of your choice - pico, kate, makes no difference as long as you create a new file of that name.
Copy-paste this text into the file:
[Default]
VideocardFs2open=OGL -(1280x1024)x32 bit
LastPlayer=PlayerName
GammaD3D=1.00
You can change the resolution by simply inserting for example 1024x768 instead of 1280x1024. Save the file, go to your Freespace2 directory, fire up the game and hope for the best. Also I would advice to select a PlayerName of a pilot that exist, I don't know what would happen if you type nonexistent player name into that field. Probably nothing, but better be sure.

Although, I don't have any idea why it wouldn't create that folder and file itself if you have run the executable... Perhaps it's a bug or something else, I dunno.