Here's the way to set the overall presentation size: http://www.rstudio.com/ide/docs/presentations/displaying_and_distributing_presentations The default is quite small: 960 * 700.
The interaction between the figure sizes, output sizes, and presentation sizes is tricky and I'm not an expert, but this seems to work ok. After some messing around, this looked alright:
first slide
======
width: 1920
height: 1080
Slide with plot which I want to fill the whole screen
========================================================
title: false
```{r myplot,echo=FALSE,fig.width=8,fig.height=4.5,dpi=300,out.width="1920px",out.height="1080px"}
plot(cars)
```