When we try to make choices, the way we make those decisions is determined by the number of options and the number of variables we need to consider. Our conscious mind is best when there are few choices and few variables. But increasingly often, we are faced with choices where we have many options to choose from and a lot of variables to make sense of. When things aren't clear, where we have many pieces of incoming information - that's when our nonconscious brain makes better decisions.
When we have too much information for our rational brain to make sense of, it usually draws upon a subset of information to base its decision on. Unfortunately, we aren't always aware that this is going on. Say, you are choosing a car. If you weren't very experienced at this, and you didn't have an experience pattern to draw upon from your nonconscious brain, your rational conscious brain might base its decision on a variable that isn't very important, like the colour of the seats. Research seems to indicate that our conscious brain can only process fewer than ten variables, and in some cases only about four. This is far fewer than the number of variables we have to consider in most situations. People often do better after looking at a choice and making an immediate decision (when their more emotionally-based non conscious brain processes the current information and integrates it with past experience and decides), rather than studying the problem over days, weeks and months, hoping that their rational conscious brain will decide.
Of course, there is a counterview that it is 'better to think than blink' (or make a snap judgement). But my sense is that a gut feeling is there for a reason. We have neuronal pathways from our guts that go way back into our evolutionary history, when the thing that made us feel bad was most likely something we ate - and the way to stop feeling bad was to purge the offending material out. Our gut reacting badly is a signal that we are feeling upset, even if rationally we can't see what the threat is - our wiring, or nonconscious nervous system is telling us something different.