If you try Evernote’s new web interface on a desktop browser, you’ll noticed that they use IFRAMEs to build their three column design with independent scrolling in each column. Unfortunately, Safari mobile on the iPad does not support IFRAME. So, you cannot scroll below the bottom of the display.
Evernote has a free iOS app that works with the iPad and iPad 2, however. So, this is mostly a point of interest for people like me who sometimes prefer using a web interface instead of leaving the browser view and starting an app on the iPad.