Janeway grew up in an authoritarian household. She rebelled by becoming ultra-authoritarian, thus demonstrating to herself her own superiority over others by her ability to strictly adhere to whatever regimen she adopted.
She is only truly comfortable around passive people. She finds the independence of others threatening to her self-image (that being that she knows better than anyone what everyone should be doing).
Through her dissembling, she managed to keep this trait hidden from her superiors, whom she served like a sycophant (thus her boast about knowing half the Admirals of star fleet on a first name basis in "Think Tank"). Her promotion to Captain was the result of these relationships, not her ability to lead others.
Her real expertise is in the sciences. When she's in a good mood she indulges this expertise with research. This fascination with science often leads her into dangerous situations where she forgets she's not in the alpha quadrant and cannot expect disaster relief in a short time.
However, her ego demands the highest accolades and science doesn't provide enough of them. Janeway expected being Captain to be a short step for her becoming an Admiral. This adventure in the Delta Quad has been very hard on her, for she's not getting the accolades she craves from superiors.
Instead, she's been forced to confront her own crew repeatedly demonstrating her superiority over them. She's grown so used to their disagreement her habit is to follow any instruction with the phrase "That's an order".
She's deathly afraid of losing command, not because she believes she is the only one who can lead them home (though she believes that too), but mostly because she's afraid of coming home and losing her chance for accolades and promotions by not being in command of the ship.
She does not handle crisis well, feeling the pressure to make -a- decision (any decision) rather than looking undecisive. And she is not good at taking advice, for fear that the credit for success will not fall on her.
One of the few influences to survive from her childhood is her desire to be a mother. It is a twisted version of what it was initially, but her frustration with relationships have resulted in her 'adopting' those under her command, interfering with their personal lives on the basis that she is 'mother to the crew'.
Her inability to accept challenge, and her willingness to crush resistance, are demonstrated in "Tuvix, "Thirty Days", and "Equinox, Part II".