This is a bug both with FTL distribution and Xorg (I think). The relevant bug reported to xorg bugtracker is here:
https://bugs.freedesktop.org/show_bug.cgi?id=70179
As I described in the link, the game crashes the whole Xorg just after completing the "Loading" bar on my Ubuntu 13.04 installation. To fix, I had to remove some files from the game installation directories (so that the system-wide equivalents are used by the game instead).
In my case, since it was installed via Steam, the files were located on "~/.steam/steam/SteamApps/common/FTL Faster Than Light/data/amd64/lib" (or replace "amd64" with "x86" if yours is a 32 bit operating system):
- libfreetype.so.6
- libIL.so.1
- libILU.so.1
- libILUT.so.1
- libpng12.so.0
- libSDL-1.2.so.0
- libstdc++.so.6
- libz.so.1
Note that there are two more files in that directory that must not be erased: libbassmix.so and libbass.so must remain there, because they are not available for system wide instalation.
One must already have those libraries on the system, except maybe for devIL and SDL. To install them, use (on Ubuntu):
$ sudo apt-get install libsdl1.2debian libdevil1c2
and the game should e able to run after removing those files.