Why do (almost) all military transports have high wings and civilian transports low wings?
For military transport aircraft:


Wings further off the ground will mean that the engines will also be further off the ground, reducing the risk of foreign object damage.
You can move vehicles under the wing, and taxi across smaller taxiways.
The fuselage can be closer to ground, facilitating transport.
No wing spar crossing the cargo floor.


Reasons why most commercial transport jets don't have it:


Many are converted passenger jets.
They are mainly pallet loaded, less vehicles and bulky objects.
They normally use prepared airports, which military jets cannot assume they will.
They often loaded from a side door, and it makes little difference I think if you go up one meter or three meters.



  but then why do civilian aeroplanes hate this design?


Airlines don't 'hate' this design, look at the BAe146 Quiet Trader for instance. It's just not that many commercial aircraft from which cargo jets are derived are built this way.


  Except in the erstwhile USSR, I haven't really seen high-winged military aircraft being used as civilian airliners (Boeing 737 size and beyond), though I can't think of any reasons why not.


Military jets are very expensive to operate and the east block Antonov 124 probably satisfy the most demand. There are a few commercial C130 (L100) around though. It's also not like the US airforce will give us C-5 Galaxy to a commercial company to do whatever it wants with it.