Our subconscious just has a way of knowing (or at least hinting at) things that we can't immediately recall or rationally piece together in the moment. We've refined it over time without even realizing it. So, I trust it first and foremost--but I try to reconcile it with any pertinent information I also have available.
But then I do everything I can to ensure that I'm not intuiting complete complete bullshit by asking questions, probing the world, introspecting, etc. Y'know, making sure the ol' compass is actually calibrated correctly.
Fluffywolf generalized the question from the OP and transformed it into one that's a hell of a lot more interesting. Kudos to him.