The reader doesn't have to agree with the setting of your story: he just has to understand it.
I'll basically answer with a longer version of "show, don't tell".
Our society may look down on extramarital affairs and multiple partners, but the reader has to understand that this is not our society.
Since the covens-clans are a big part of your setting, you should give yourself time to describe them, exploring every nook and cranny of their culture before moving on with the actual plot. Better still, show this through the actions and thoughts of your characters.
Your characters were born in your society: for them, this matriarchal structure is the norm. It will become normal for the reader too, since the reader "perceives" the story through the eyes of the characters (or through your external narrator, if you're using that).
Of course, it will be strange at first: things will happen that the reader won't understand outright. You may open the very first chapter with the fifth marriage of a powerful witch, with the four previous husbands attending the event like it's completely normal.
A mother's brother is considered the true fathers of their children, and spend more time raising them than a biological dad.
So, uncles are the real fatherly figure of your world. You may show how children seek this figure and tend to suffer when it's not there. The term "uncle" doesn't indicate a strong emotional bond and "mother's brother" is a clunky definition, so you could create another term relevant to your society and make characters use it:
Alice: You seem really close with Charlie.
Bob: He's my insert-term-here. Of course I am.
Alice: Ah, I didn't know. I grown up without one and it was a harsh.
Decide a set of core values for your society and keep in mind that they will influence every aspect of day-to-day life. Think your characters accordingly.
Back to the reader: if you do this well, in due time the reader will understand what the basic rules in your story are. He may still think that our society has better cultural norms, of course: but remember that you don't need to convince him.
You just need to explain how things work in your world, be coherent, and he will roll with them.
Being coherent means, for example, that men will more attached to the sons of their sisters rather than their own.
After all what you're trying to do it's not different, let's say, that authors writing about magic, high-tech sci-fi, paranormal events, incredible creatures and so on.
When you meet dragons in a fantasy book you don't jump to the conclusion "Hey, dragons ain't real, they don't exist in this world, how can they be in this story". You just acknowledge they are a thing and go on.
So it's a matter of suspension of disbelief: it will work if you can keep it.
On a side note, I wouldn't struggle to make this alternate society of yours seem like a positive thing. Like most cultural norms, it has upsides and downsides. If you show both equally, you're creating a more believable world, and the reader will be more enthralled by it.