You would think they would.
But this does not surprise me at all. Multitouch makes it difficult for the browser to tell if you want to select, scroll or drag and drop which is of course entirely omitted. You have to double tap to get the dialog box then tap again to select, tap to activate a control, tap and hold to get the magnifier so you can position the cursor precisely. Way more tapping than what would be required if you were using a mouse.
New gadgets take some time for web authors to get used to and you can bet the majority of web pages, including Apple, were not designed with the iPad browser in mind. Still, the limitations of the iPad browser are similar to those of the iPhone and a lot of work has been done to make things look right on iPhone. Often that entails a watered down version of the site. If a site toggles back to "desktop mode" when it sees your iPad rather than staying in "iPhone mode", there are bound to be things that simply don't work. Did you provide feedback to Apple about this?