Apple stands firm on not supporting Flash on iOS - if you use Flash, your site visitors on iPad, iPhone, etc. will not be able to see your content.
Is that a big deal? I don't know, but the fact that over 14 million iPads have been sold, I would think it's a pretty big deal.
Of course, this is just my opinion, but at this point, I would shy away from using Flash on your site and rather choose to use the updated capabilities of HTML 5.