Quoting Crystal Zhu's answer from my msdn thread here
As far as I know, VS will not be able to instrument the binaries for apps running on IIS, we can’t collect code coverage for the app hosted on IIS as we normally do in VS2013. There are some approaches to accomplish your requirement. Reference ‘IIS’ section in this blog: Collecting Code Coverage Data when Running Web/Load Tests
And AkshayGarg provided us detailed steps to collect code coverage for a web app/website published on IIS from running coded UI test in this thread: http://social.msdn.microsoft.com/Forums/en-US/57496eb5-6c36-4eb0-9f14-5a72562fcae6/how-to-get-right-code-coverage-in-coded-ui-testing?forum=vsautotest . You can try it.
Actually we also can collect code coverage metrics for ASP.NET applications running on Internet Information Server when we run coded UI tests from a lab environment in MTM.
Reference: Walkthrough: Using Code Coverage in Microsoft Test Manager