If you happen to have Adobe Acrobat Pro, what I do at work is export my PDF with all of my layers turned from ArcMap and then open it up in Adobe Acrobat Pro. Go to the Layers view on the left, and right click on a layer you want to be turned off by default and choose Properties. In properties you can set the Default State from "on" to "off". Then just save your document and it is ready to go. If you don't have Pro, maybe Nidhin's link will help you sort it out in ArcMap.