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
Although changing the fonts used by AI works well, an alternative is to restrict ggplot2 from using Dingbats in the first place by adding the argument 'useDingbats' to your ggsave command eg:
ggsave(plot=p,height=6,width=6,dpi=200, filename="~/example.pdf", useDingbats=FALSE)