Google never wanted Motorola so that they would be tied down making hardware. It's clear they were after their patents as leverage in protecting Android partners. I am sure those patents brought Apple to the negotiating table, and some sort of agreement was made to co-share them in exchange for not going all out attack on Android manufacturers.
If Google wanted to make hardware too, trust me you would get a killer Nexus machine, but where would the benefit be in that when all the other manufacturers throw in the towel and go back to trying to make their own OS.
As for Samsung specifically, why wouldn't Google be pleased for their success? Firstly we have a company that shows that if you couple good design with marketing, you can achieve enormous success with Android. On the other front we finally have an Android manufacturer that has the ability to compete with Apple, putting out phones that are not only every bit the equal of iPhones, but in my own personal view - better.