Apple did find a solution in mobile Safari for touchscreen hover states on the Web. However the Web platform generally offers more affordances for accessibility than Flash ever did, which I'm sure helps.
This is possible in HTML because it's trivial to determine whether or not a :hover changes display or visibility properties of other elements. As you've supposed, Flash did not afford browsers with that sort of ability.
TBF one thing Flash did manage to achieve was the proliferation of web sites and apps that were as hard to use for people without protected disabilities as for people who did have them.
Whether this increased empathy for people with disabilities is an open question