All text for plots is antialiased, but certain symbols are not. For example, pch=1 and pch=19 look great, while pch=16 and pch=17 look terrible. This problem exists in the x11 window, and not when rendering as PDFs.
plot(1:10, 1:10) # empty circles; looks good
plot(1:10, 1:10, pch=16) # solid circles; looks terrible
plot(1:10, 1:10, pch=19) # also solid circles; looks good!
Unfortunately, ggplot2 uses the pch=c(16, 17, etc.) symbols as default in geom_point(), so this is affecting many users.