Well for starters, that's not really a valid comparison, because Microsoft keeps at it in online services because they think it will be profitable in the long run - not because its helping some other division.
That said, Microsoft DOES take heat after every earnings release for the performance of online services, and their stock has suffered accordingly, so I'd say you're proving my point, really. Its not the individual shareholder like you or I that makes noise - its the people from big investment firms and analysts that cause the uproar over these things.
Anyway, if it is in Google's best interests to improve the Motorola brand, they will. Considering the amount of profit Apple's smartphone unit generates, I'd say it is. And more importantly, whether you agree that they'll favor Motorola or not, you can't fault HTC/Samsung for being wary of this, and not fully believing Google when they say that's how it will be.
Google's history is full of them saying "no no, don't worry, partner with us on this, we aren't trying to subvert you", only to do so a few years later after they've grown. A prime example is Youtube - Google swore up and down that they weren't getting into the content business, so the media companies should let their shows on Youtube. Slowly but surely, Youtube is expanding its reach, now they're renting movies, how long until there's a movie or show that's exclusive to Youtube?
You can certainly make the argument that its in their best interests to keep Android on a level playing field, and maybe for awhile, they will - but that doesn't mean its going to stay that way.