I am only posting this because I couldn't find the answer anywhere and figured others might run into the same issue.
If you are getting this error: "Could not load type MvcApplication", look at the Output path of your project and make sure it is set to 'bin\'. The problem is that the AspNetCompiler cannot find the files if they are not in the default location.
Another side effect of changing the output folder is that you will not be able to debug your code and it comes up with a message saying that the Assembly info cannot be found.
Hope this helps.