The whole idea that because the military does something it must be acceptable, is a rather strange one.
The military uses black boots because they will only issue one boot. Black goes with Green, Blue, Red, Black and almost any colour that an infantryman is likely to wear. Unlike SFers the army wont issue another piece of kit base on style.
It is also worth considering that no one in the army wears Chinos. They wear khaki coloured dress trousers. Neatly pressed and with a military heel. The black shoes coordinate with a black weapon and usually dark headgear (I'm thinking berets in green or red). On SF we strive for our accessories to be in tonal range with everything we wear, thus if we have a multitude of black or dark accessories then black shoes may look acceptable. 99% of the time however black shoes will be the only example of black in the outfit and as such stands out far too much, better to have the shoes in the same tonal range as the trousers than have them as an anomalous intrusion.