I created several simple ggplot2 plots and saved them to PDF files using the following commands:
p <- ggplot(plotobject, aes(x=Pos, y=Pval),res=300)
ggsav
This seems to be a perverse problem in which Adobe Illustrator cannot find a font (AdobePiStd) that is distributed with Adobe Reader and thus is likely present.
If you search your computer, you are likely to find it. On my WindowsXP system, it was in: C:\Program Files\Adobe\Reader 10.0\Resource\Font
After finding it, you can install it and other fonts in that folder, which should enable Illustrator to find them.
For other font/pdf problems in R, the embedFonts function in grDevices package is useful.