This is a big question, but simply put:
Witchcraft is a study and practice of spiritual forces through natural objects.
Wicca is the name of a religion that uses witchcraft, but does not believe in any dark force, nor Satan, only positive energies.
The Goddess (in this topic) is what many witchcraft users believe in. The Goddess is only a female entity worshiped and used to balance out the energies by a male God as well.
I believe it is all frowned upon today because this all was practiced in such secret after the Salem Witch Trials event, that everything practiced was not exposed.
Kind of like if Gospel singing or spiritual healing in some churches weren't exposed, all of those people would look weird as well if they were not known much about. It is all frowned upon because Hollywood, and other story-tellers created false tales of witchcraft in the manner that it seemed scary, odd and unrealistic, and all-around a bad thing to do because you would bring about earth trolls, monsters, or demons.