it's the runtime

There's nothing novel (or, indeed, appealing) about C# the language. The process of executing C# bytecodes, however, requires peculiar, patentable operations that would probably be impractical to implement another way.

If MS did begin to assert patents, everybody would suddenly need a C# equivalent to Gcj, which might not help if many people have come to depend on bytecode libraries for which they don't have source.