To get a handle on what the MVC pattern and how it helps web applications like Cake, you could read up a bit on the framework that inspired Cake: Ruby on Rails. Ruby on Rails is a web framework for the programming language Ruby. It implements both Active Record and MVC. The article Rails: What goes where? explains the file structure of Rails, which Cake shares - there is no Rails code in the article.
Model View Controller is a software design pattern described by author group Gang of Four. Dean Helman wrote (an extract from Objective Toolkit Pro white paper):
"The MVC paradigm is a way of breaking an application, or even just a piece of an application's interface, into three parts: the model, the view, and the controller. MVC was originally developed to map the traditional input, processing, output roles into the GUI realm.
Input -> Processing -> Output
Controller -> Model -> View
"The user input, the modeling of the external world, and the visual feedback to the user are separated and handled by model, view port and controller objects. The controller interprets mouse and keyboard inputs from the user and maps these user actions into commands that are sent to the model and/or view port to effect the appropriate change. The model manages one or more data elements, responds to queries about its state, and responds to instructions to change state. The view port manages a rectangular area of the display and is responsible for presenting data to the user through a combination of graphics and text."
You can read more about the MVC pattern in this article - MVC: Most vexing conundrum