I took an undergrad class on European Witch Trials and would be happy to provide some sources when I get home. It was really a fascinating course that I feel lucky to have been able to take.

Ideas of magic were of course much older than the 16th century, and many dated back to different pagan/folk traditions, especially in more the rural communities of western Europe. It's not as relevant to the question, so I won't expound upon those traditions/ideas but can do so if requested. The Malleus Maleficarum was one document that systematized a lot of these beliefs into a more cohesive theological theory, which the scholastic/monastic communities would then go out and 'preach' to the lay people.

The acceptance of this magic was not at all at odds with Christian belief (at least not in the minds of the average person) since the experience of magic was perceived to be an almost daily occurrence. Especially when it comes to negative outcomes, such as famine, sickness or other forms of calamity. So when these bad things happen, the obvious reason is that the devil intervened. Why would the devil intervene and why would God not stop it? The most common answer would have been punishment for some sin. But what sin, and who is to blame?

So imagine you're living in a 16th century farming community in the French countryside. You're most likely god-fearing, and so when disaster strikes and the annual harvest is almost fully stunted, you look around your community for an indication of who might have brought this disaster upon your community.

The answer at this time was to look at those who deviated from a typical Christian, god-fearing life. These would be outsiders, people were marginalized and stood more apart from the core of the community. And most commonly, these people tended to be women: widows, spinsters, folk medicine practitioners, and others. After all, they are convenient scapegoats with nobody to support them or their defense.

So you, the 16th century peasant, take notice of this woman who is not married, does not have children, has no political or economic connection to the community, and possibly practices some folk traditions that lay outside of what the locals consider to be typical Christianity. And then you consider what you've been hearing from 'learned' theologians: stories of women sneaking off to commune in the forest with other women, performing sacrifices to the Devil, engaging in orgies, women who've sold their soul to the devil (think Doctor Faustus) in the form of some kind of worldly magic. Magic...that was then turned on the community they were at odds with.

So yes, you can say that the idea of patriarchy has something to do with it, because these women had such a low social status that such horrendous accusations could be lobbed at them without fear of rebuttal or reprisal. And at the same time, there's a whole theological structure that has been built up to support this idea of magic, evil and witchcraft.