I don't consider it a phobia for myself, but I have a fear of windows at night. I'm afraid of who might be outside and able to see me when I can't see them.
I remember when it began I was 4 and 2 walls of my room had windows. My mother thought it would be neat to use very sheer curtains. Nothing ever happened, but I was spooked and scared since.
She might be afraid that something will crash into the skylight and shattered glass will fall on her--which could be why she's asking if they will hurt her.
I have no idea why she is afraid she wont tell me she just does not like them.
We are planning to add on in a few years and were talking about putting in skylights (this was before we knew of her phobia) 
I actually sat in the car for like 15 minutes, hoping they'll leave but they never did. I just couldn't bring myself to open the car door to go outside, and ended up driving to another grocery store. Is that pathetic or what?