The subservience of women to men was a common theme in early Christian writings -- an outgrowth of both traditional patriarchal attitudes and the extreme hierarchical nature of the church itself. Groups which did not hold to hierarchy in any form were attacked immediately. There is no shared authority between the genders in traditional Christianity, either in the church or in the home. Homosexuality would be particularly threatening to this ideology, as it raises the potential of redefining gender roles, especially in the home.
Witness how the recent attacks upon homosexuality in society has progressed hand-in-hand with the mindless promotion of vague "traditional family values," particularly those which "put women in their place" and reinforce male dominance in the home. With a married couple of two women or two men, who exactly is supposed to be in charge and who meekly obedient? Never mind that the Christians who fear such relationships will never be asked to make those decisions themselves -- the mere fact that people are making such decisions on their own rather than obeying someone else's religious proclamations is quite enough to give them fits of apoplexy.
The perception of women as inferior to men, and possibly the enemy of proper religious or social order, has survived down through this day in the most conservative and fundamentalist religious movements around the world. Religious institutions and doctrines are a primary repository for ancient beliefs about the social, physical, political, and religious inferiority of women. Even if the rest of society is moving on and improving women's status, religion remains a main source of beliefs and attitudes which retard that progress in the hopes of reversing it completely. And, where women cannot be attacked directly, they are attacked indirectly through negative stereotypes about "feminine" values as compared to positive stereotypes of "manly" or "masculine" traits.
It would be a mistake to assert that the Christian persecution of witches and witchcraft was nothing but an attempt to suppress women and feminine influences. Christian society, politics, and theology at the time simply wasn't that simplistic. At the same time, it's hard to overestimate the role misogynistic attitudes and repressed male sexuality played in the persecution of witches. It seems likely that if they didn't exist, the extreme violence directed at women and alleged witches probably wouldn't have occurred.