Such as the two angels in the Allegory for Good Government.
Was this because of the Greco-Roman muses?
Your question postulates an argument, which is that the Middle Ages and Renaissance were 'misogynistic', by which I assume you mean the people of the time. What exactly do you mean by misogyny?
I can't speak to the Renaissance much, but I can speak to the Middle Ages. There were a lot of things that were personified as women in the Middle Ages. Women at their best were usually signs of virginity, purity, honesty, truth, faith, basically all the good virtues you would want to have. The greco-roman muses didn't really have much to do with the inspiration for this (although the Renaissance artists would revive this tradition). Most medieval artists and writers eschewed the classical traditions in favor of more modern practices. Mostly it was just that there was a lot of symbolic importance given to women.
There's also a theory that women were communal objects. Since they were not given much of a say in anything in their lives, they were viewed as an indicator of the relative virtue of the community. If a woman became pregnant out of wedlock, it reflected poorly on the community. Conversely, if a woman was a faithful and dedicated mother and wife, it reflected well on the community. This could have fueled the trend you are talking about, but this theory should be taken with a grain of salt.
Also, Medieval society was not wholly misogynistic. It is an oversimplification to say that. Sure, women were not afforded a lot of the freedoms they have today, but it was not misogyny in the same sense as we have it today. There were plenty of Medieval women who were very prominent and revered. Julian of Norwich, a Christian Mystic springs to mind, as well as Margery Kempe.