to be clear: in zappa's universe, everybody is stupid.
it is true: the women are often portrayed as not so bright, but they aren't generally portrayed as less intelligent than the men, who are also generally portrayed as fairly daft. at the least, they tend to have names and personalities...and they often win out in the end....
so, if you're just focusing on his treatment of women, you're really missing the plot. it's a total attack on the 60s culture in general, not a targeted attack on the women within it.