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
EDIT 2018 The question under was for the initial confusion face. The answer to this question is pdf(useDingbats = FALSE) as stated in numerous answers above. I won't delete this answer, in case you want to read about fonts (which might become a problem too).
OLD ANSWER AI does not recognize Helvetica type fonts. In my computer it doesn't matter that much, since it automatically replaces the font with something suitable. Of course you'd want to change the font in some cases. I often do it manually in AI (just select all the text and change the font type). Here is a thread on how to change the font in ggplot2: Modifying fonts in ggplot2
Ps. There is also another thread that might be helpful: Fonts in R plots