You just have to specify in the JMS Template rule that you defined to build the slave site that you want a "copy" for the "robots.txt" file instead of a Symbolic Link.
So go in the JMS Template menu and edition the rule that you created.
In the template, select "folder and files" tabs where you have the list of all the files and folders for which you can defined the action.
See also the tutorial video 0.b slide 30 to 34 that explain some values in the template rules.
www.jms2win.com/en/tutorial#jms12x-0b