Except PhoneGap is not really the best of both worlds. Users prefer native apps because of the quality and consistency of the user interface frameworks available to developers. If you're building your app with HTML/CSS and deploying it within a PhoneGap container, you don't have access to UIKit to build your interfaces, you're still rolling your own which leads to huge inconsistency, not to mention it's within a UIWebView which is much slower than native components.
Just because the app is in an executable and not a URL doesn't mean it's a "native" experience for the end-user.
I think they do, for a lot of things at least. There certainly are some things that desktop users prefer in a browser (I see way more desktop users using Facebook in a browser than via a native app, even though native apps exist), but if I think of the apps that I see people using day-to-day, there's a huge swath that aren't in a browser and it's not clear to me will be in the foreseeable future.
I mean, browser-based email has gotten really good... yet there are still a ton of people that use native email clients. Hell, I and lots of other people even use a native Twitter app on our computers - if there's anything that seems replaceable with an in-browser app, it's Twitter.
Replacement of many native office/productivity/image/media apps with in-browser apps seems a long way off to me. And it's not just because HTML doesn't yet fully provide rich/"native-feeling" capabilities, it's also that people don't want to run all their apps in rectangular browser tabs — maybe OSes will evolve to not be as app centric so that all of a user's in-browser apps won't be organized under a single icon in their dock/taskbar (though I wouldn't bet on it), but I don't see a lot of movement toward that. I wouldn't be shocked if 20 years from now everything's HTML, but it sure doesn't seem like it'll happen in the next 5.
Just because the app is in an executable and not a URL doesn't mean it's a "native" experience for the end-user.