Linux sites need money and that's not easy to squeeze out of "Free Software" enthusiasts (and a large number of Linux businesses are run by enthusiasts).

Microsoft has a definite interest in keeping their name on Linux sites that may be visited by non-enthusiasts thinking of defecting - it gives them greater credibility in the Windows / Linux controversy.

In my opinion Microsoft is not wasting their money and the sites are not betraying the community - they're getting the money they need to serve that community.

In the end this levels the playing field just a bit so both sides have to compete more on value in each others camps.