Having been in the military, I'd have to say that the policy came about because of a 'few bad men'. If I had to guess, I'd say that at some point some soldiers had some type of party or something at the hotel that got out of hand and at that point it became company policy to not provide rooms to soldiers.
While that might not be the case here, this kind of thinking (or really lack of thinking) always pisses me off. "We just had a party where everyone was tall and they trashed the room. NO MORE TALL PEOPLE!"