Here's the relevant code:
ggplot.3plus<-ggplot(summary.3plus, aes(x=sp1, y=fract.mean, fill=ForestAge)) +
geom_bar(position=position_dodge())+ coord_cartesian(ylim = c(1, 1.175))+
geom_errorbar(aes(ymin=fract.mean-se, ymax=fract.mean+se),
width=.2, # Width of the error bars
position=position_dodge(.9))
ggplot.3plus<- ggplot.3plus + theme(axis.title.x = element_text(colour = "red"))
You can see that with the last line of code, I can change the color of the axis title, but not the color of the axis LABELS.
What about
ggplot.3plus + theme(axis.text.x=element_text(colour="red"))
See ggplot2 wiki page for more theme details.