I think (though I don’t personally suffer from this) the issue is the gondola system appears more unsteady than something like the monorail.
My wife will hop aboard a plane. No problem. Go in a tall building, no problem. Use a ladder, no problem. Hop on the monorail, no problem.
She won’t get on a Ferris wheel to save her life, though that would be a very odd set of circumstances. Similarly Tower of Terror is not something she will do willingly.
The gondola is the same thing.
For lack of a better way to describe it, it’s not a general fear of heights, more of a fear of perceived unsteady conveyance. She also gets nervous in elevators.
I think folks like her are going to have an issue with the Skyliner, but Disney will be Disney and find a way to get the guests to their destination. Might be free minivan rides. Might be a small shuttlebus. Might be a single regular bus being reinstated, but they won’t leave guests... pardon the pun, hanging high and dry.
I’m personally excited for this project, it’s grown on me since we found out about it, and look forward to riding it in the future.