It looks like that TuxGuitar fails to set the proper clef.
Just find the music in the lilypond file and put \clef "G_8" in front of it. That will do the trick.
Explanation: As Tom_C correctly points out, guitar is written in treble clef but one octave higher than it actually sounds. TuxGuitar apparently just sets a treble clef (or no clef at all, which amounts to the same). The systemic way to handle that is to use a treble clef with a small 8 under it (which says that everything has in fact to be played one octave lower). That's the clef that Lilypond knows under the name of G_8 (or treble_8).
Setting the proper clef will also make sure that Lilypond will both "know internally" the correct notes and typeset them correctly, too. You could just transpose everything an octave higher; however, if you for instance played the MIDI generated by Lilypond, it would also sound an octave higher than it should.