Pano2VR or Flexify are probably your simplest solution, but if you're a scripting geek and have to use Hugin tools, then scripting nona commands is the way to go.

Since the panoguides board went down in sea of spam, I go to the Internet archives and post DorinDXN's answer (with some minor edits) of a Windows .bat file to create six nona_gui scripts and run them to create the six cube face images.

This is the equi2cubic100.bat file.

You'll need nona_gui.exe from the Hugin distribution. In the same folder with nona_gui.exe, place the pano.tif that is the equirectangular file.

You can change w1500 h1500 with the desired cube-face dimension in pixels w6000 h3000 with the size of the equirectangular and v100 (100°) for the FoV of the cubic.

Each line starts with @, don't break it into sublines.

@echo press any key if pano.tif was produced by PTGui
pause
@echo.
@echo -----------------------------------------------------
@echo Generating Face_0 FRONT
@echo p f0 w1500 h1500 v100 >script.txt
@echo m g1 i2 f0 m0>>script.txt
@echo o w6000 h3000 f4 p0 r0 v360 y0  u10 m0 n"pano.tif">>script.txt
@nona_gui -o cube_0.tif script.txt

@echo.
@echo -----------------------------------------------------
@echo Generating Face_1 RIGHT
@echo p f0 w1500 h1500 v100 >script.txt
@echo m g1 i2 f0 m0>>script.txt
@echo o w6000 h3000 f4 p0 r0 v360 y270  u10 m0 n"pano.tif">>script.txt
@nona_gui -o cube_1.tif script.txt
@echo.

@echo -----------------------------------------------------
@echo Generating Face_2 BACK
@echo p f0 w1500 h1500 v100 >script.txt
@echo m g1 i2 f0 m0>>script.txt
@echo o w6000 h3000 f4 p0 r0 v360 y180  u10 m0 n"pano.tif">>script.txt
@nona_gui -o cube_2.tif script.txt
@echo.

@echo -----------------------------------------------------
@echo Generating Face_3 LEFT
@echo p f0 w1500 h1500 v100 >script.txt
@echo m g1 i2 f0 m0>>script.txt
@echo o w6000 h3000 f4 p0 r0 v360 y90  u10 m0 n"pano.tif">>script.txt
@nona_gui -o cube_3.tif script.txt
@echo.

@echo -----------------------------------------------------
@echo Generating Face_4 UP
@echo p f0 w1500 h1500 v100 >script.txt
@echo m g1 i2 f0 m0>>script.txt
@echo o w6000 h3000 f4 p270 r0 v360 y0  u10 m0 n"pano.tif">>script.txt
@nona_gui -o cube_4.tif script.txt
@echo.

@echo -----------------------------------------------------
@echo Generating Face_5 DOWN
@echo p f0 w1500 h1500 v100 >script.txt
@echo m g1 i2 f0 m0>>script.txt
@echo o w6000 h3000 f4 p90 r0 v360 y0  u10 m0 n"pano.tif">>script.txt
@nona_gui -o cube_5.tif script.txt
@echo.
@del script.txt