The confusion arises from how we perceive the word 'Good'. Here it is used in the archaic sense of 'holy' or momentous.
Good Friday, called Feria VI in Parasceve in the Roman Missal, he hagia kai megale paraskeue (the Holy and Great Friday) in the Greek Liturgy, Holy Friday in Romance Languages, Charfreitag (Sorrowful Friday) in German, is the English designation of Friday in Holy Week source
In other words, Good marks the uniqueness of the Passion. It affirms the centrality of the crucifixion and resurrection to the Christian faith.