Noticing that the Microsoft link that you referenced is dealing with J#, if you're happy with Java, then go with it.
The switch to .NET is the same as with switching to any other programming paradigm. You go with the flow and hope that you don't get caught in the whirlpool.
Take Java as an example. Sun, while still buying up other smaller companies, may be a prime candidate for purchase by someone else. If that someone else is like IBM or HP, the software side of Sun may be spun off to a new company that will have to compete directly with Microsoft and Borland (plus all of the many Linux/Unix software providers out there). On the other hand, if it's bought by Microsoft, Borland, or even Novell, the software may be incorporated to that company's own offerings. Because Java never made it to true open standards status, anyone acquiring Sun could even squash Java like a bug.
Microsoft, while not the greatest of companies, can probably provide one some confidence that it will still be around within the next ten years. Granted, .NET may have morphed into something else, but, then again, what language hasn't. I'm sure that you would find more AcuCobol users today vs. users of the original version of mainframe COBOL; more FORTRAN 90 users than FORTRAN IV; more Visual Basic users than QuickBasic, etc....
I truly believe that one should never reject a programming paradigm based on how one feels about its manufacturer/distributor or about the way it works. Personally, I wouldn't want to program in COBOL; but if I have to, so be it.
Overall, programming should be fun. Whether you're using .NET, Java, or FORTRAN (yeah, I still like FORTRAN), if you like it, keep doing it. If you happen to get a paycheck along way, so much the better.