Why are minerals found in "large" quantities and not scattered throughout the earth as individual atoms?
First of all, Earth is not a random assortment of atoms. While it probably formed along like that in the beginning, somewhere along the way it differentiated into distinct core, mantle and crust, which are not chemically the same. That's a story for another question though, and there is an excellent answer to it on this site.

Back to your question, Why are there ore deposits?

So in addition to the Wikipedia quote given by farrenthorpe, here are some more (hopefully easily digestible) points:

Chemical elements posses differing properties. Even if you take a random mix of all elements in the periodic table, each and every one of them will have different properties. 

Imagine a homogenous pile of gold and salt. Now, start pouring water over it, let it flow to a specific place and wait until the water dries and evaporates. Exploiting the different chemical properties of Au and NaCl, you've created two "ore deposits", one of gold and the other of salt. In the Earth, there are a multitude of processes resulting from all kinds of combinations of temperature, pressure, fluid chemistry, magma processes and more, that facilitate selective concentration of certain elements over other elements.

If you are interested, here are some answers regarding the deposit formation of gold and rare earth elements.