Brian Flemming has done a bunch of work looking into the matter:
While books endorsing religion receive evaluations that use terms like "marvelous" and "engaging," virtually all books from an atheist perspective get negative or, at best, dispassionate reviews from Publishers Weekly, using terms like "intolerant," "ineffective" and "simplistic."
...Publishers Weekly reviews matter. They most often appear as the first review listed on Amazon.com, for example, providing the very first opinion many people will read about a given book. A marketer would call that valuable "mindspace," and that marketer would be right. Does one of the most influential contributors to Amazon.com have a prejudice against atheists?
Brian was able to find negative or problematic Publishers Weekly reviews of God is not Great, The God Delusion, The End of Faith, and even I Sold My Soul on Ebay. I was able to find similarly negative language in an article about "anti-religion books"
...this fall brings a striking number of impassioned critiques of religion—any religion, but Christianity in particular—and calls for a return to reason rather than faith as a guiding principle. ...Several other books this season assert that religion is not only unnecessary but negative. ...Other voices call not for an end to faith but for a more measured and examined one, and for greater understanding and respect across faith lines.
Source: Publishers Weekly
On the other hand, I did find a "positive" review of Nica Lalli's Nothing: Something to Believe In:
Lalli's adds something fresh to the mix: rather than being an angry apologetic, it's an engaging personal account of non-belief. Raised in Chicago and New York to free-thinking parents who seem to have provided little supervision, Lalli had sporadic encounters with religion at her friends' churches and synagogues as a child. ...Although Lalli got along well with her Christian mother-in-law, her self-righteous sister- and brother-in-law were a different story, and much of the memoir's second half explores serious family tensions. ...Lalli doesn't come across as being quite as open-minded as she claims to be, she does see herself as an equal-opportunity agnostic, as skeptical about a tarot reading as she is about Christian platitudes.
Source: Publishers Weekly
Even though this is a positive review, there are still plenty of swipes against atheists: it's not "an angry apologetic," her freethinking parents seem to have "provided little supervision" when she was a child, and Lalli isn't "quite as open-minded as she claims." Which seems more plausible: that all the atheist books reviewed really are as bad as the reviews say, or that there is a bit of an anti-atheist bias at Publishers Weekly? The latter strikes me as a more plausible explanation for what we're seeing, and kudos to Brian Flemming for both noticing and brining it to everyone's attention.
Consider contacting Publishers Weekly to ask about this. If you do write to them, please copy your message here in comments so others can see what is being written.