As discussed in this thread, the PDF spec allows for layers to be locked, this means that when the file is opened in a PDF reader the user cannot toggle the visibility of those layers. It would make sense to put general information (in the case of a map: logo, legend, title, grid, map collar etc) on locked layers and only have the user control the map data layers.
Right now FME doesn't support this, we have to do this in Acrobat after the file is created, but obviously that's not an option for high volume or automated processes.