It does not seems that emacs started with –daemon read the .Xdefauls resource it seems that the only way setting it is by the default-frame-alist variable.

I have my setup like this :

(setq default-frame-alist '((font-backend . "xft")
                            (font . "Inconsolata-14")
                            (vertical-scroll-bars)
                            (left-fringe . -1)
                            (right-fringe . -1)
                            (fullscreen . fullboth)
                            (menu-bar-lines . 0)
                            (tool-bar-lines . 0)
                            ))

PS: inconsolata font can be installed from the package ttf-inconsolata