I think it is also important to remember that mono is both a virtual machine runtime (the JIT compiler, garbage collector, etc.) as well as a collection of class libraries that run on this framework (the System.Linq namespace, the XML parsers, etc.).
The majority of the .cs files you see are part of the class libraries. These are basically C# code that run like your own C# code (with some exceptions, but basically it doesn't make sense for everyone to reinvent and re-distribute the wheel over and over, so these are the C# "base" class libraries). This is why you can download complex mono programs as such small file sizes if mono is already installed on the machine.
For mono, the JIT, runtime and garbage collector are largely written in C/C++ as you would expect. If you ever get a low level error, you will often see GNU debug tool dumps as you would in C, just with lots more useful information. The Mono framework is very good at taking any C# code and converting it to CIL code that can run anywhere, and they use whatever toolset is best suited to ensure the code does run anywhere (which in this case meant a C compiler runtime on linux).