If people _insist_ on making phone apps as websites, there's Cordova and all that. Such apps are never very good, of course. I still haven't seen a website-based desktop/phone app that wasn't a clunky non-native-looking resource-hogging mess.
Why not? Because they can actually be extremely useful. Such as for receiving emails, Facebook messages, Slack pings, or news updates you've subscribed to. Maybe somebody tweeted you. Any of these apps could work as progressive webapps.
Regardless if the platform is native or web-based, the feature remains opt-in. If you don't want them, then don't subscribe to them.
There are some more coherent arguments in play, don't get me wrong (in particular, the argument that web apps are a bastardization of what the World Wide Web was intended to be for; I agree with that wholeheartedly), but a lot of the rhetoric around here really reeks of elitism.
The webapp ecosystem is making the same class of mistakes pure-Java UIs used to. They assume e.g. that a textbox is just a rectangle on a screen that you can type stuff in. But it's not just that; it's much more.
Each operating system has a large set of default UI behaviours and idiosyncrasies. Continuing the example, a native textbox may be a clickable rectangle accepting keyboard input, but it also has a set of well-defined behaviours for Tab-cycling, text navigation, right-click handling, keyboard shortcut handling, cut/copy/paste handling, etc. Web applications fail to replicate that functionality completely and consistently. And platform consistency is a feature - one that many users value.
On top of that add resource waste (spinning up a webview and parsing heavy markup languages just to show a bunch of buttons) and web-specific failure modes - many vendors do not care about making their webapp work correctly when connectivity is limited, spotty or lacking. Hence the occasional full-screen 404 or 501 or connection-lost error when you press a button.
I want my applications to be performant, platform-consistent and interoperable. Web apps fail at all three, hence I avoid them like the plague, and discourage everyone from developing them.
About the only benefit I, as a pro user, I get from web application is the relative ease one can reverse-engineer their backend APIs with.