Fuko is very stoic, and in general is not the kind of person who would probably be able to cry in front of others. It took her almost until the end of the route to really even know how to lean on Tomoya or Nagisa a little, and she seemed to be aware that people were going to forget her impossible existence anyway. Because of this Tomoya is our main point of reference for the emotional side of things - the way that reader is more in tune with Tomoya emotional creates a sort of feeling of watching over Fuko as opposed to being directly involved. I think it worked, but I can see how some people might not have gelled with it.
