The Book of The New Sun is one of Wolfe's more contraversial post-modernist experimentations in narrative structure, in which it is hard to judge each volume on its own; -to be fair, I feel one should read the cycle as a whole and judge it as a whole.
...and as to the accusations of misogynism, I don't really see much misogynism in Severian's sexual escapades as much as in his continual judgement of women as being "weak" and his continuous harping on this theme, which does come across as pretty much a machismo attitude, and which I think might be Wolfe's own attitude rather than just that of Severian's - I'd have to re-read other works by the author to be sure of this, though.
As for the 'machismo torturer' image, (Severian leaping bare-chested and cloaked onto the execution stage under much applause, for instance) I do think some of that is a tongue-in-cheek jab at stereotypes as well as a bitter look at the fascination many humans seem to feel with gore, horror and death - therefore the sick adulation that Severian gleans from the populace who love to watch him kill.
Let's face it, all of us have some kind of emotional reaction towards death, and death is indeed a topical subject for us all, as we all have to face it sometime or another.
It's also a subject which has fascinated the creators of literature since the beginnings of literature itself.
Wolfe does an interesting "take" on death, memories and immortality in the idea of continued consciousness through other humans via the rather repellent and unsavory ritual with the Alzabo gland.
Talking of stereotypes, I had consistently thought of Jolenta as the typical sexually charismatic narcissistic movie-star type (male or female) who believe they are God's gift to the opposite sex. This image was confirmed for me, and expanded to the cosmetic surgery and botox enhanced crowd that one finds in celebrity circles these days, at the end of the book when a bit of a 'reveal' on Jolenta is done. It seemed to me as if Wolfe is expressing an opinion of initial disgust which is later tempered with pity when he shows the emotional and psychological vulnerability that this type of person often carries with them behind their public masks.
I'll reserve final judgement of the series until I've re-read the last volume, which I'd read long ago as a teenager, and on which I'm pretty sure my opinion might have changed in the meantime.