This document deals with the issue where you've added your solution to TFS, but the TFS icons are not showing up in solution explorer therefore appearing like the project isn't under source control.
You've already tried to go to Tools->Options->Source Control->Plug-in Selection, and selected "Visual Studio Team Foundation Server". But still it appears like its not under source control.
Click on File-->Source Control-->Change Source Control. In the Change Source Control dialog, check the server bindings to ensure they are setup correctly. If there are issues with the bindings, you will see red squiggly lines under the server names - or - if there are no bindings at all, you will see "<No Server>" in the Server Name/Binding columns.
If you see "<No Server> click on the "Bind" button. If you've already added the project to source control then it will automatically bind them. At this point it will ask you to check out the Solution and Project file, do so and then check it back in. You should now be set.
If you see issues in this dialog, you can unbind each of the projects by selecting the project and clicking the "Unbind" toolbar button. Once you've unbound the projects, you can rebind them by selecting each project and clicking "Bind".
If you still have issues, you might need to reinstall VS and see if it works.