Hi,
Yes of course you can use the command line to launch OptiFDTD simulator.
The simplest way is to launch the simulation window corresponding to your type of simulation (2D or 3D) and giving it your project file path as a parameter. For example, if I have a simulation file called test.fdt in c:\sim\, I can type the following command in the command window (or in a batch file):
"c:\Program Files\Optiwave Software\OptiFDTD 12\bin\OptiFDTD_controllerSim3D.exe" c:\sim\test.fdt
If you want to give a specific script to execute, you can use more advanced command lines. They are give in appendix D of the user manual