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They never really explain why he's so scared of her. Soran, the only other El Aurian we really see in any great amount, doesn't seem to have any special abilities that might make Q scared of him. I don't see how living for centuries and being temporally-sensitive would scare Q.
That always bugged me, among other loose threads. I'm guessing by now, there's some beta canon that goes into it. Maybe it's that she's been around long enough to remember his bad hair in his youth:
Emergency! (1972)
They clearly had originally intended her to be...MORE than what she turned out to be.
I really wish they had either stuck with the original plan, or just left her backstory mysterious.
Edit: Or at the very least, something better for her than her species being pretty good at listening...
What did you say?
That, uh, you have no chance to survive make your time?
Wasn't he powerless in the episode he was afraid of Guinan? Maybe he was worried she would use the opportunity to get revenge.
Nope. He had his powers. He even offered to get rid of her. But he was still scared of her. He makes some very weird claims about her. She also has her hands raised like she's about to do something powerful with them.
https://www.youtube.com/watch?v=lJdJfyDn_Ck
Basically it all got retconned.
They also don't explain how the Q are omnipotent, just that they can play with reality. Ex: change the coefficient of gravity IIRC the meteor scene.
Beings that live somewhat out of time or whatever that other dimension thing Kirk got stuck in (been a long time since I watched that movie), I guess you could make the case that there may be some tangential mojo between both of those mechanisms that could be dangerous to a Q.
But that's a lot of wand waving. It was never explained because each of their powers is supposed to stay mysterious.
The Nexus from Generations is seperate from the Q, just a recurrent timeless dimension that travels along a spacial ribbon which some of Guinan's people happened to interact with.
As for the Q Continuum, according to Q (de Lancie) "The Q didn't come into existence. The Q have always existed." VOY s3e11 "The Q and the Grey"