Exit any instance of the browser and change your preferences file, located in $HOME/.mozilla/firefox/xxxxx.default/prefs.js, where xxxxx is a randomly generated string specific to your installation. The entry you're looking for is "browser.startup.homepage". Restart the browser.
Code:
sed -i 's/user_pref("browser.startup.homepage",.*/user_pref("browser.startup.homepage","www.site.com");/' $HOME/.mozilla/firefox/*.default/prefs.js