Lyric discussion by powertothehavenots 

Cover art for Smooth Sailing lyrics by Queens of the Stone Age

Seems this song is about people ignoring consequences and doing as they please then reasoning behind religion. "God only knows" is used twice. On one occasion he suggests doing what you like and if you can reason it with god your ok:

Well god only knows One long vacation If reason is priceless There's no reason to pay for it

Then another occasion he is feigning a pious sense of right and wrong:

God only knows So mind your behavior Follow prescriptions Of your loaded savior

Reminding you to reason your behavior according to your chosen faith. Then he suggests possible reasoning for doing what you like:

Every temple needs gold Every hook needs to shine

The "smooth sailing" is just used as a depiction of no one getting in the way of what you wana do and ignore the fear and disregard getting caught "I'm in flagrante In every way, every day".

For my money this song seems government directed