Easier to Load
As stated earlier, this is your primary reason. You have to be able to load in cargo from the ground. If you want to get troops and vehicles in fast to somewhere with minimum equipment, you want to be able to roll them of the aircraft, and the lower the aircraft, the easier this is done.
Shorter gear is stronger
The longer you make the gear, the more it will bend. Bad news if you're trying to land on rough ground.
More Cargo space
The shorter you make the gear, the less trouble you have finding space for it inside the aircraft, where you want to maximise the amount of space you have for cargo, especially for vehicles and the like. The anatomy of a cargo aircraft is that they are typically hollow inside, unlike passenger aircraft where they fold up into the center section.
Landing gear is heavy
Landing gear is very heavy, since its got to support the weight of the entire aircraft above. The shorter you make it- the lighter the aircraft gets.
Better use of ground effect
The low gear may bring the aircraft a little bit closer to the ground, maximising ground effect and lowering your landing speed, again very ideal for rough terrain.
Note: These don't only apply to military aircraft, but to a lot of commericial ones as well, since the benefits are the same. Look at the Dash-8, ATR 42/72, BAe 146 along with the rear-engined planes, and they all try to do this for these reasons, although ease of cargo loading might not come first on the list.