You can import GeoPDFs into Golden Software's Surfer program and maintain the referencing. You can then export it to a GeoTIFF, and still retain the referencing in the TIF file. There is a free trial version.
To quote @TimSpivey:
"The Federal government, in its infinite wisdom, is decreeing that we should all move to GIS.
The USGS, in its infinite wisdom, is releasing its topo maps in GeoPDF format.
ESRI, in its infinite wisdom, has not built GeoPDF support into ArcGIS Desktop.
The G-Raster program, which is supposed to be able to convert GeoPDF to GeoTIFF, cannot do it in its current version (6.3) as of today's date
Adobe Acrobat X Full Version cannot export to GeoTIFF"
I know your question was in 2012 and the above saying was in 2014, which makes them rather old in technological years. You would think with all the stuff ArcGIS Pro and ESRI can do these days, they could have at least one tool that can import a GeoPDF, or a even a regular PDF. I know I can easily convert a pdf to a jpg or png on windows or mac, but can't ESRI also do that?
On that note, I need to get back to learning about how to convert a GeoPDF to a proper .kmz file that properly works with Garmin, turkey season is upon us ha!