I suspect you didn't read the second book of the Kushiel's Legacy series (Kushiel's Chosen) because she writes a very thinly disguised Jewish community in it (the Yeshuites). Yeshua, the fictional equivalent of Jesus is mentioned in the first book and (spoiler warning!) half the Yeshuite community takes up arms and goes off in search of a holy land (paralleling the founding of the current nation-state of Israel). In the third book she delves even more into Jewish myth and writes about the finding of one of the lost tribes and the ark of the covenant.

Also, the Lions of Al-Rassan mentions the Jewish people in a equally undisguised manner (the Kindath). I'd argue that the book is not quite fantasy (not much supernatural stuff) but it's different enough that it's definitely not an alternate history. I class it with fantasy simply because of the tone of the writing and because it's set in the same world as several others which do have supernatural events.

I don't think authors deliberately avoid writing about Jewish characters so much as they see no reason to include the religion/people unless they're going to contribute something to the story. If no one was writing them it would be unusual but as it is I suspect it's more that stories in which Jewish people would be written about/in to aren't that prevalent.