You can have your web app not show the safari bar when saved to the home screen. If you're using a framework like jQTouch it's automatic, and combined with a custom icon and splash screen really does give the 'native app' feel.
It's just a pity that it's so awkward to get it onto the home screen. Prompting the user to press the '+' and save it is clunky.
But you still have to deal with stuff like having to login every time. Losing some screen space of your app to the Safari bar at the top, etc.