I think the argument is that every native application is effectively something akin to facebook's walled garden.
1) sharing data between apps is near-impossible, unless format converters are written (they never are) and explicit manual steps are taken.
2) linking between apps is impossible (e.g. you configure an address for a client then click/tap on it to navigate to said client when the application is not made by microsoft).
3) searching across apps is impossible. You can't just go to google.com, type in what you remember and have it show you the app.
4) native apps are expensive, because they never have a huge market (compared to online apps).
5) native apps are really badly supported.
6) you can't give anyone else access to your data (easily, just look at how long it took microsoft's army of developers to give office some semblance of real sharing. And it's still not up to par).
7) anyone you want to give access to a doc now has to buy your (expensive) mobile app.
I'm not saying you're wrong, just that you are forgetting quite a few facts here. Native apps are usually self-contained, small, unmaintained things. Yes, that does have some advantages, but it also has large disadvantages.
I would even agree with the "ads are good for you" argument to some extent : these companies are "spying" on you in order to attempt to create (theoretically) win-win economic transactions. Essentially they show you stuff you want, in order to make you want to buy/have/rent/... it. That is good for you (you get "value" in the economic sense), the other side gets some money, and a small "tax" is paid to the intermediary. Economic activity goes up, and it becomes easier to get a job, ... etc. Of course this argument only holds for pay-for-transaction ads (ie. not for banner ads, not for things like facebook, essentially only for google's model).