That was my reaction. I would think that by publishing the ECMA standard (and there have even been revisions to the original standard), they have pretty much given up any patents on C#/.NET. Besides, if Microsoft was going to use their patents against open source projects, what would stop them from going after closed-source software as well?
Also, is there anything stopping anyone from writing an open source JIT that compiles C#/VB.NET/F# to Java bytecode? Or, converting .NET bytecode to/from Java bytecode? Then, you wouldn't be locked into a single system.
I'm actually working on a new open source project right now that is written in C# and is going to be released under either the BSD or MIT license (I haven't decided yet). So I probably couldn't disagree more with this article. I think that if more open source were written in C# or Java, it would be much easier to port Linux (BSD, etc.) to other platforms, since most/all of the software that people will want to use doesn't even need to be rewritten for that platform.