As someone who is fairly involved in the writing/publishing community, there was a very obvious explanation that stuck out to me when I read this article:
She's writing about typical shit. Publishers don't just buy books, they buy authors. They want to sign you for several books. If she's writing about a 26 year old girl trying to find romance and a career in NY, no one wants to read that book by a 26 year old girl. It's typical. It's everywhere. No agent would get excited about that. Or a book about teenagers who find out they have magical powers. Or a book about a rich white woman who goes on an international journey to find herself.
Have those same stories written by a 40 year old man? It's different. It changes the sell. One of the first things I learned about query letters is that the writer has to show why they are the ones to write this novel (when any publisher could probably give the same idea to a very talented, cheaper, ghost writer). It's more interesting when the author is either very qualified (a geologist writing a book about mysterious, disappearing rocks in a Maine mining town) or contrary to what one would expect (a Pakistani immigrant who writes about a white family during the Great Depression).
This is like a man getting rejected for engineering jobs then claiming sexism because he got more responses when he put a female name on his resume. Publishing is dominated by women. Like, as in completely and utterly. Most readers are women, most editors/publishers/agents are women, and a very high percentage of published work is by women, including the majority of bestsellers.
2/3rd of the NYT bestsellers are women. Her book just isn't that good.