I would agree that "makes" should stay singular to correspond to "what," even if the subject of the sentence is plural. However, I think "fruit" is singular. I can't think of a context in which I would say "fruit are." Here are some sentences that are okay, in my opinion:
Fruit is what makes this dessert special.
Fruit makes this dessert very special.
Cherries are what makes this dessert special.
Cherries make this dessert very special.
A single large grape is what makes this dessert so very special.
A single humongous grape makes this dessert unforgettable.
Fruit is important for a balanced diet. OR Fruits are important for a balanced diet. (But I much prefer the singular.)