Well, actually they can, as Twitter has shown. It looks like Apple is trying to pull an Internet Explorer on us though.
Web applications are fine, and have their place. I'd argue that place is not as frequently-used, heavily interactive applications; native apps exist for that, and are better in most ways.
This is the thing – some publishers insist on using their stupid application when all I want to do is browse some content. Other publishers insist I use their shitty JS-HTML-Hybrid nonsense because they are too stingy to develop proper applications. I wish we could learn to more effective use technologies in the right places.
> This is the thing – some publishers insist on using their stupid application when all I want to do is browse some content.
That's exactly the problem PWAs solve. Those publishers want some features that on iOS are only available to native apps, and so have to make the experience suck for Apple users by using an installed native app instead of a web app. Both publishers and users have an aligned interest there for PWAs, which goes against Apple's own interest.