Someone sent me over a link to download the sample standard asp.net MVC sample, I noticed that there were 2 web.config files:
/Views/Web.config
This is not your application’s main web.config file. It just contains a directive instructing the web server not to serve any *.aspx files under /Views (because they should be rendered by a controller, not invoked directly like classic WebForms *.aspx files). This file also contains configuration needed to make the standard ASP.NET ASPX page compiler work properly with ASP.NET MVC view template syntax.
/Web.config
This defines your application configuration.
This is from the book Pro ASP.NET MVC Framework