Keeping it as far away from where applications have their menu makes a clear distinction to the user that each is for controlling something very different.
Applications are controlled by menus at the top, the system is controlled by menus at the bottom.
Mac has also experimented with this dual concept. For instance the applicaitonapplication dock is at the bottom, and open apps are placed there. But the application specific behaviour (not minimising, closing) are kept in top menus.
But mainly, the reason the taskbar is at the bottom is artbitrary, it's been there since Microsoft first added it in Cairo. Now users expect it, so to keep a consistent and predictable interface it is adhered too. See more about menu conventions for windows apps here.