As you can read here their response to the EU antitrust lawsuit http://techcrunch.com/2015/04/14/internal-google-memo-respon... google makes the argument that users spend a lot of time inside apps. I would expect they are worried about the ability for users to go directly to content and bypass search from which they make money.
I'm not sure which side of the fence I fall on. The web is arguably a more open technology than native apps but the experience in a native app is often better.