I made a video-how to use the TFS Administration Tool
I get a lot of questions about setup problems, and they're regularly related to a missing user permission. The Team Foundation Application Tier is (typically) composed of IIS Web Services, SQL Reporting Services, and Windows SharePoint Services. Loosely speaking, adding a user through Team Explorer will only set the permissions for the IIS portion-an administrator still needs to set the permissions for the other two components.
You can go into Windows SharePoint Services and SQL Reporting Services and grant the permissions in separate steps. MSDN has a section on Managing Permissions, including some how-to examples for common groups:
If you'd like to use one interface to manage all three permissions at the same time, you can download the TFS Administration Tool from CodePlex. The user will need the right to grant permissions on all three systems. I have a quick walk through in the following video: