It's that you can't spy on your user nearly as effectively with a web app compared to what you get with native. You're limited to web APIs, instead of native APIs. Which is why, I believe, there is a full court press on so many sites to get mobile users away from websites and into their apps.
I'm not alone in preferring to just use a website and not clutter my phone with apps for every online site I may interact with. Yet many sites actively press me to switch to the app including crippling the mobile version of the site. Removing features that work fine on desktop as soon as they detect a mobile client.