The difference is that each environment for non-Web apps - Mac, Windows, KDE etc - has each own somewhat well defined look and feel, that applications should follow in order to feel native. That's not true for Web apps in different Web browsers - they are supposed to look the same. Qt compromises that native experience by letting you target multiple platforms. For Web toolkits, at worst you'll end up with an app that doesn't stand out (e.g. by using Bootstrap) but certainly not with one that won't blend in.
I don't know if you've used Qt or not, but one of the things that always impressed me about it was how good it was at defining the abstraction just right at the level so that out of box each platform's app did in fact look right on that platform and fit in with the same look and feel. Obviously that doesn't catch everything, but the areas where Qt apps didn't fit perfectly into the platform's native look and feel by default, it was always easy to insert some platform specific code to go in and call a few functions that brought it up to the level you wanted to see it get to. You know I'm not going to say it's exactly 100% as it would be writing a whole separate app for each platform, but it gets shockingly close with shockingly little extra effort, and as someone who helped write an app using Qt and OpenGL to run on Linux, Windows and OS X on a short timeframe, Qt was amazing.
We're not talking about write once look the same everywhere here like old Java/Swing or a webapp. That's just not what Qt does unless you twist its arm. By default it compiles a version that's intended to fit in on that platform target you compile towards.
And seriously. A webapp compromises the native experience much more than a Qt app would. Pretending you can avoid that by stuffing your stuff in a web browser where there are no cohesive look and feel standards that make any sense and that this is somehow supposed to yield a better user experience?
I've used Qt a lot. In fact, I'm still a big fan and wasn't trying to sound negative about it in any way. I absolutely agree that Qt does a tremendous job at abstracting away the differences but still, it's the little details that matter and no toolkit could address them all. Things like ribbons on Windows. Multi touch support, cover flow and proper OS X-like multiple window management on Mac. Not to mention mobile. For big applications, these glitches add up and in no time you find yourself resorting to way too many native workarounds.
But my main point was to that cross-browser Web toolkits and cross-platform GUI toolkits are apples and oranges. On the Web there are no UI guidelines. It's essentially free for all. The chrome of the Web browser constitutes a clear separation point between the native experience and the Web experience, which makes it possible for things like Gmail not to feel hostile on Mac, Linux, Windows and any other Web-enabled environment. Whether or not that's good for UX is irrelevant, the fact remains is that Web apps have never tried to integrate seamlessly with the look and feel of the host environment and the users have grown accustomed to that.
