True, although if Flash had stuck around long enough (i.e. if iPhone hadn't signed it's death warrant) I'm sure eventually we could have come up with a solution for a11y.
Most of the flash sites that I really remember consuming were actually very simple documents that relied on flash for presentation, so it would be easy to provide a screen reader friendly version of the content.
Also a lot of flash content was cartoons and games which don't lend themselves to screen readers anyway.