Spain has the best cubic Pyrite in the world

I know that the crystal structure is primitive cubic, but I don’t see how cubic structure on the molecular level translates to cubic structure on much larger scales. If you are given some number of cubes, there are many different ways to assemble the cubes face to face, and only one of these ways is to create a large cube. So why is it that the pyrite in this rock forms nearly perfect cubes?

Spain has the best cubic Pyrite in the world. Here is a large natural cubic crystal completely formed with all 6 sides. The faces are highly lustrous with only a few minor edge nicks and one slight contact line where a second Pyrite once just the slightlest lay against this one

All completely pure primitive cubic crystalline compounds will form macroscopic, perfect cubes. Deviations in macroscopic form are the result of impurities somewhere in the molecular lattice, otherwise a low cohesive energy such that the chunks of material don't stay together well (e.g. by electrostatics).

 Perfectly pure $\mathrm{N}\mathrm{a}\mathrm{C}\mathrm{l}$ forms cubes likewise, but smaller ones, because the cohesive energy is lower (if I'm not mistaken). Thus the energetic affinity of a material for itself (over available impurities) increases probability of perfect macroscopic formation that models the crystal unit-cell. 

Most compounds attract foreign species though, so nicely perfect cubes of any cubic-structure chemical are hard to find -- even of pyrite, as mentioned in the other answer. Lots of materials form surface oxides before expanding a macroscopic version of the unit cell; others bond with similar ionic "pieces" -- e.g. contamination of 

K+$\mathrm{K}{\phantom{X}}^{+}$ in NaCl$\mathrm{N}\mathrm{a}\mathrm{C}\mathrm{l}$ to form chunks of rock salt, KCl$\mathrm{K}\mathrm{C}\mathrm{l}$.

NaCl$\mathrm{N}\mathrm{a}\mathrm{C}\mathrm{l}$ crystal is used as an optic barrier for samples in infrared spectrometers because when pure it can be shaped linearly in any dimension to form any desired (semi-)planar shape with atomic precision. Effectively you can remove one atomic layer at a time because it's a pure two-component cubic macro-system.

I remember when I traveled to the Dead Sea in Israel -- there were really nice, big (like 1-inch), perfectly formed salt cubes on the shores. I have some pyrite at home too. It's cubic but some chunks form out in different proportions and directions due to impurities/chemical environment.

Boleite cubes on hardened mud matrix

Table Salt

Fluorite

https://chemistry.stackexchange.com/questions/29330/why-does-pyrite-form-cubic-crystals
http://www.lehighminerals.com/cgi-bin/dbase/views_record.cgi?dbase=/home/lmineral/public_html/cgi-bin/auctions/dbase/archive/12302005.txt&fielda=53&fieldb=52