Running an ASP.NET Web Application on Apache with Mono
You need to install mod_mono on Apache. There is more information about this on the Mono ASP.NET page. The .cs is compiled into the DLL is not needed at run-time.
The .cs files would be compiled into the DLL, so they are not needed for deployment. Other than that, we would probably need some more information to figure out why the app won't run under Apache/Mono.