I use FlashBlock, and block all Flash by default. Then I just override it for Flash elements I actually want to see. That, and, I do a lot of browsing on iPad now...
When you use ClickToFlash, it still loads the Flash objects, it simply doesn't show them until you tell it to. To the websites you visit, you're still a visitor who has Flash installed.
I want websites to know that I don't want to view Flash content, that's why I go without the Flash plugin altogether.