It can, but hasn't. Our prejudice against short people is almost certainly a result of past associations with malnutrition and poverty. I can't speak for other reasons, but this reason for short stature is no longer a main cause in modern Western (or even Eastern) society. Plus what you say about the fickleness of advantage/disadvantage equally applies to tall stature. Maybe Ryanair will start charging tall people extra next month.

Your comment shows your hand on your prejudice, because you're still somewhat commenting from the viewpoint that tallness is still an inherent positive trait. That clearly didn't work out for the dinosaurs. I'm not saying the opposite is true (that shortness is an inherent positive trait), but I do believe we need to dispel our preconceived notions because they are very short-sighted.