I was struggling getting FlyWithLua to show up at all in my X-Plane 12, and I saw no mention of it in the Log.txt either. After inspecting with ldd I realised the plugin binary looks for libglut.so.3, which was not on my system.
The Debian package libglut3.12:amd64 provides the following files:
/usr/lib/x86_64-linux-gnu/libglut.a
/usr/lib/x86_64-linux-gnu/libglut.so
/usr/lib/x86_64-linux-gnu/libglut.so.3.12
/usr/lib/x86_64-linux-gnu/libglut.so.3.12.0
As one can see, libglut.so.3 is not part of the default symlinks deployed. After creating it myself, FlyWithLua started working fine.