iTune's layout is just following Apple Human Interface Guidelines. They define the standard window layout for an OS X application to ensure consistency between applications and make the user experience easier.
The guidelines define what a toolbar and a bottom bar are :
A toolbar is useful for giving users immediate access to the most frequently used features in an application. Any item in a toolbar should also be available as a menu command. An application-wide toolbar in its own window is also called a tool panel (or less frequently, a tool palette); for more information, see “Panels.” This section describes toolbars that are part of a window with other content.
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A bottom bar is a window-frame area that is below the window body. Bottom bars give users access to controls that directly affect the contents or organization of the window body.
In general, controls in a bottom bar are frequently used, but are somewhat less important than controls in a toolbar. For example, the bottom-bar controls in iChat allow users to add buddies to the list and to text message, call, or video chat with a selected buddy, whereas the controls in the toolbar are focused on the user of the application. Figure 14-25 shows the iChat bottom bar.
I do not think there is a clear usability advantage to put player controls on top of your application window, but when there is a standard in a given environment you must consider it. Consistency and standards are very important when designing an interface because they cut learning time for your users as well as making them more comfortable.