The thing is when you double click the WMAppManifest.xml, Visual Studio opens it up in a manifest editor which doesn't expose the Protocol ability. You have to open it in Notepad to modify it. Here's what the MSDN arrticle says:

>> To register for a file association, you must edit WMAppManifest.xml using the XML (Text) Editor. In Solution Explorer, right-click the WMAppManifest.xml file, and then click Open With. In the Open With window, select XML(Text) Editor, and then click OK.