If the iPhone shows us one thing it's that no matter how crap something is, Apple can market it well.
Regardless of that however, there's still the more blatant issue of the problem with proprietary browsers and platforms that actually prevent widespread adoption of web applications. We still have no agreed standard on what access to hardware a web application should have, if it's limited some applications wont work, if it's open you have a security risk. Web applications developers also already face the issue of non-standards compliant browsers and everyone's to blame there including Microsoft with IE, Mozilla with Firefox and Apple with Safari - none of them correctly implement the various web standards and a proprietary platform and browser only increases that problem. So even if we are going towards the whole web applications route with mobile devices an open platform and open standards shared by all device manufacturers is still the way to go - if only for the sanity of web applications developers such that they don't have to write!
The point is, the more we move to web applications the more the browser and OS are tied together or at least forced to communicate so that the browser can do the things it needs to do to be able to support as wide a range of web applications as we have standard applications.
Finally, It's also worth noting that some applications certainly wont even work over the web, specifically applications that have to shift large amounts of rapidly changing data such that a networking connection can't handle the amount of resources shifting back and forth - many modern games for example. All these are reasons why an open OS is still important - to ensure standardisation across the industry so you can be sure your applications be they web or normal are accessible on whichever mobile device you use.