That being said, there are both native and browser games that are great, just like there are some that are mediocre. The browser is imho a great place to prototype a game, make a first game as a newbie or even publish something that's not too resource hungry.
I'd even go as far as saying that WebGL will stimulate the development of native games as well. WebGL based game development is a lot closer to native game development in a way than Flash games are (at least from my limited experience) so new developers might make the switch more easily when their needs exceed what the browser can give them. Exactly the position John Carmack's company is in, although they never had the modern browser at their disposal in the past.
These are exciting times and I suffer a little bit inside whenever I see talented people arguing over them instead of making the best of them.