Going where the money is
The reason for this change of heart is the Azure platform, which means Microsoft can profit almost as much from hosting Linux applications as from Window
There is probably already even more money to be made from hosting un*x* on Azure as hosting Windows and, over time, focussing on the Linux subsystem might mean that MS can get out of the expensive OS development game. In this you can see echoes out of Lou Gerstner's pivot with IBM away from OS/2 (wonderful though it was) into making sure that Notes, Tivoli, et al. ran on client systems.
* For example, MacPorts has a CI instance running on Azure.