Because many devices still lack decent hardware acceleration. If you're doing a lot of complex UI work with tons of CSS3, some devices just can't keep up. My team investigated building one of our recent apps using only HTML5 and CSS3, and while it rendered smoothly on some newer devices, it performed terribly on older ones. So for compatibility and performance reasons, we moved back to native. Perhaps this is simply anecdotal, but in our experience, your milage may vary when it comes to building mobile web apps, sometimes it's the best option, sometimes it's not.

Because it's easier to charge for apps. And actually get paid.

Also, these are phones -- performance is still important.

Also, can't do infinity blade in HTML 5.

Also, the UI and experience are better in apps.