I think most referees give a foul in most of these situations because it's usually merited. In the majority of cases, the defender has carelessly caused contact with the attacker. The law says that it is careless when a player "shows a lack of attention or consideration when making a challenge or acts without precaution." If the defender wanted to, they could easily choose to exercise care and act with precaution so as not to make any contact with the player in front of them, by slowing down slightly or altering course slightly away from them in the other direction, instead of crossing behind them. By continuing on at the same speed and/or crossing behind the opponent in such a way as to cause contact, the defender has, at least in most instances as far as I'm concerned, acted carelessly - as that is defined in the Laws of the Game.
As I said, they often do this while using a totally natural running action but believe me, it's the easiest thing in the world for professional athletes who are in full control of all their bodily movements, to just slightly clip the heel of a player running in front of them while making it look like a complete accident.
