Forking is the underlying source of freedom in open source software -- if you don't like something the current managers of a project are doing, fork it.
If your open source code is licensed under a non-copyleft license like Apache or BSD, Microsoft (or any other entity) can fork it and use it commercially regardless of whether you are a member of the CodePlex foundation.
The CodePlex foundation asks that member projects assign the copyright to the foundation to allow them to defend its intellectual property from a legal perspective. Through the right to fork, open source licenses ensure that the code itself is owned by the community-at-large, and whether the CodePlex foundation "owns" the code from a legal perspective is meaningless.
I understand people being skeptical given Microsoft's checkered past with open source, but at least give them a chance to prove that they've changed.