Mono is tolerated by Microsoft, and supported behind the scenes (not financially or anything, more like cheerleading) because it lets MSFT tell enterprise customers that "See: You aren't locked into Windows - there's a Linux alternative that you could use."

Microsoft is not setting technical direction for Mono, and I expect that there are few (if any) Microsoft employees contributing to the project -- because of conflict of interest and IP concerns. They are very much at arms-length with regards to Mono.

So far as *nix tools being superior - I would agree that they do what they are designed to very well. But don't turn up your nose at C# and the .net framework -- it's quite good, and doesn't have the Java factory factory factory issues.