One thing that I discovered the hard way about SQL Reporting Services running in SharePoint integrated mode is that it DOES NOT SUPPORT HAVING ANONYMOUS ACCESS ENABLED IN SHAREPOINT.
After setting up and configuring SharePoint 2010 and SSRS, everything was peachy until I enabled anonymous access on the SharePoint web application. When doing so, SSRS would still run reports and such, however Report Builder could no longer connect to SharePoint/SSRS.
There is no work around for this, on the SharePoint/IIS web application that you are using SSRS with you cannot have anonymous access turned on. If you require anonymous access to some of your SharePoint content, it must be on a different web application.
Hope this saves some headaches out there as it took a while for me to figure out that was the issue.