As a librarian (and parent), I find it incredibly frustrating when I can't sell a book to a reader who appears otherwise interested in it but is embarrassed by theover. There are plenty of boys out there who are fine with reading a book with a female protagonist (Hunger Games, anyone?) but are turned off by a girly cover and the connotations it brings with it. This situation applies to girls and "boy" covers as well. Girls may not be embarrassed by the covers, but they can certainly find them unappealing.
Maureen Johnson addressed this issue in a tweet to her readers, issuing a challenge to imagine how the marketers at publishing companies would present books if their authors were of the opposite sex. Check out this link to read more about it, and be sure to watch the slideshow. It made me laugh and also want to cry!