The iPad, just like the iPhone and iPod Touch before it, doesn't support the Flash plugin. Steve Jobs has
come out saying it's a dying technology, and likens it to dropping support for floppy disks.
I am already building sites with iPhone, iTouch and iPads in mind. None of these devices support Flash BTW. That's not to say I'm doing this for every client, though.
Suffice it to say you cannot please all of the people all of them time. Find out who your target audience is and build accordingly. It's not much different than deciding which screen sizes to build your pages for. Don't use Flash for really important content such as menus or contact forms. Use HTML or DHTML equivalents. Offer your visitors choices.
If media is a big part of what you do, start learning HTML5. I predict the new <audio> and <video> tags are going to send Flash to the rear of the bus without help from iPhone/iTouch/iPad.
Video For Everybody (VfE)