Answer: I do believe this is a question that is different for each person, but I can give you what I believe it means:
They don't fear that they do not have enough power, but that they have too much power, and that power is unstoppable, even by the speaker.
Hence; "It is our light (too much power), not our darkness (the lack of power), that most frightens us."
Explanation: I have no context, so I did a general meaning. If this is incorrect, please write some context of the story/speaker this quote comes from and I can revise the answer.
Hope this helps!