I don't mean to be crass, but if you use the search feature you will find there are many many many many threads on Flash work arounds, reasons why Flash doesn't work natively ,etc.
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One interesting alternative to iSwifter, is to use a remote desktop app and then watch the Flash on your PC remotely. I use SplashTop and it works great. There's a free, limited viewing time, version so you can try it out to see if it works for you. It allows you access to your PC on both your local home network and - using a new experimental feature - from anywhere on the Internet. You'll find lots of current threads on iPad Forums about Splashtop. I had no trouble setting it up at all and I can now access my PC when I'm on the road using 3G or WiFi via a hotspot. It's a great way of retrieving files that you've accidentally left on your PC too - but the ability to (occasionally) watch Flash sites when there's no alternative or download files from the Internet, when Safari won't allow you to do it, is great.