There is something convenient in having something to download to the device and read off-line. This allows people to read their newspapers when they're flying, traveling abroad, or simply in a dead zone for their Whispernet connection.
Those mobile sites are pretty sweet, though. I don't really like the Kindle subscription deals (too expensive for the limited content available in the digital editions) so I'll have to try those out on my Kindle when I get back to the states. I'm living in Japan right now so it's not too handy unless I'm using wifi on my iPod Touch.