Many 'witches' were just the wise people, men and women, 'one estimate places men as the victims in about 15% of cases', who understood nature, seasons, maths, biology, astrology....some of them may have offered healing, knew herb craft, knew how to plant their crops at the right time. Those that didnt, who maybe weren't as lucky to of inherited that knowledge became jealous of their crops and gains and accused the wise ones of witchcraft of which the new tax collectors were happy to dunk in ponds and burn to death because self sufficiency didnt support increasing tax collection. The rise in witchcraft trials can be related to the birth of capitalism and the new wave of religious zealotry and sexism.
Many, many people were genocided during the reformation years under the guise of 'witchcraft'. Extreme feminist theory claims up to 9 million across Europe. I think thats probably more than were but it was a genocide and it is also important to remember that people are still being killed for 'witchcraft' in developing countries to this day. Some witchcraft is very dark, murdering albino children for magic is not cool.
Some believe the word witch comes from the word wicce which used to mean wise.
I personally refuse the label witch, though I have been considered as such and took the label when younger and studying paganism and druidism but now, I am just a woman who respects the natural world and tries to be wise. 
What some used to call magic is now called science as we understand our world more. A mixture of both is a beautiful thing to have in your life and the pagan appreciation for a goddess is certainly empowering for women especially in the western world were religion is very male centered around one god and thats it. Eastern goddesses are worth a look at too, they have some amazing characters like kali, shakti and tara. Check 'em out.