From the article:
the .NET Native runtime [is] a refactored and optimized CLR
According to the article, the .NET Native runtime is a (not yet complete) implementation of .NET. This means that Wine + .NET Native = a Microsoft-built .NET runtime on Linux. This is good news because this may be a way to take those .NET technologies missing from Mono, such as WPF, and still use them on Linux.
Another reason this is good news is, we're one step closer to being able to develop Windows installers in .NET. Lately I've been using NSIS and it is the most stupid, idiotic language I've ever used. It's been described as a mixture of PHP and assembly.
Another thought: the article doesn't seem to mention it, but judging by the design, the .NET Native compiler may be able to compile any .NET DLLs and EXEs, not just C# ones.