I think it is a good idea not to disdain our whispered doubts. When our most cherished thoughts and emotions face off against the bedroom ceiling at 3 a.m. and the question arises, "What if it's all bullshit?", I think it's a good idea to honor that thought. Not revere -- just honor.
It seems to me that it is our doubting Thomas who has the capacity to inspire a determined effort ... to find out for ourselves if our most cherished thoughts and emotions are worth the cherishing.
Elevating our skepticisms won't do any more than elevating our certainties will do -- that's just a surrender that invites a comforting lethargy. But when we find ourselves cherishing one god or another, one worry or another, one relationship or another, one belief/disbelief or another, then it is time to investigate and find out ... not just paper things over with more cherishing.
Honor the skeptic's sly whispers. Like as not s/he is suggesting something worth knowing. But only you can know that.