In windows if you double click on the mothur executable (make sure to download the windows version) it should open automatically. Alternatively, start up the command prompt (in task bar under all programs -> accessories) and go to the right folder (cd ) and just type in mothur (no need for a command). This works for windows XP, havent tried on other OS.

If you look up the latest version of Mothur (1.33.3 unless the new version has already been released) there is a GUI (graphical user interface) version. In order to be able to run it you will need the latest Java version. Once you have downloaded the GUI version you can just double click the executable "mothurGUI". You can then look in the "Analysis" window on the left hand side and select the appropriate pipeline and you will see a list of buttons with command names in the "Pipeline" window. Just click on them one by one and fill in the boxes. If you don't know what to put in for any particular function/command, just go and look it up on the Mothur website where there is a lot of advice and where they explain why default values were set.

I am also normally not a big fan of command line commands but for mothur I found this approach easier to use than the GUI.( I also use the Windows version of mothur, just not the GUI.) I found it very helpful at the start just to simply follow the SOPs of the Schloss group that are published on the mothur Wiki (for 454 or MiSeq sequencing, depending on your platform). The steps of the SOP are quite well explained and always have links to other parts of the Wiki if you want/need to know more about a certain command. If you then come to a specific problem or question, best ask those questions in the mothur forum - Pat Schloss and his group are very helpful and always quick to answer those questions.