Your subject line is a separate question from your post LizaM, but I'm assuming you specifically want to convert a Flex application into HTML5 and not something natively iOS.
If the Flex application is complex and you need to convert to markup that you can work with for further development then you might not have any options other than to get your hands dirty and start from scratch. Good ol AJAX/HTML (or call it HTML5 - whatever sexy words you want to use for the markup you're using to run on Safari).
There are tools out there (e.g. Swiffy and SoThink SWF Decompiler), but I don't think they'll help much if you're trying to convert rich Flex library classes. I could be wrong about this, but that seems to be the state of affairs at the moment.
J