There is a browser in their app store called skyfire that renders Flash content. Other than that, I think the onus is on the Flash developer to port their stuff over to ios.
I think apple is just trying to protect their income. They are getting away with it because they can as their branding and cult following is very strong.
As an alternative to how you can have a look at this solition: http://www.tuaw.com/2011/02/01/flash-friendly-skyfire-browser-for-ipad-gets-updated
I hope this helps.
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