The doc covers the bottom of each application that is not maximized.
Particularly in an application like the terminal, I need to get work done in that part of my screen. As you see in the image, my prompt, where I have typed "echo 4," is simply covered by the dock. I then have to manually resize the window just to get it out of the way of the dock.
I know I can automatically show/hide the dock, but I'd rather it was visible, yet not interfering.