Recently we upgraded to MiniProfiler version 2.0.1 from v1.7, and since then we have not been able to use it in our MVC3 website because when it tries to get its resources,
I had a similar issue and what I did to fix it was change the application pool to 'integrated' and then I added this new line below to my web.config and it then worked.
Here is what the complete web.config looks like now for mini-profiler.