Guinan, perhaps her whole species, is able to understand the 'correct' state of the universe. Take for example in Yesterday's Enterprise she knows details about the 'other' universe. The universe as it was during the rest of the series with the Enterprise as a ship of peace, not a ship of war.
This is, essentially, the counter power to Q's ability to alter the universe at will. It suggests that the power the Q hold is transparent to Guinan. She can see through their alterations to the mechanics of those actions and the state of the universe before those actions. Possibly, she can counter their magical technology, although that's just conjecture.
Just being able to understand the 'true' state of things would be enough to limit Q's power, which would be frightening to him. And what the Q do to the universe would be equally as upsetting to Guinan.