Respostas:
A resposta de Wilfried Thuiller na lista de discussão R-SIG-Geo funciona:
#getting a raster
library(raster)
f <- system.file("external/test.grd", package="raster")
f
r <- raster(f) #r is the object of class 'raster'.
# replacing NA's by zero
r[is.na(r[])] <- 0