For me, I always use the content server feature to transfer books to my reading devices.
Just ensure your computer and your Nexus 7 are in the same network. Then open Calibre's content server feature.
Now run the web browser on your Nexus 7, input [your computer's IP address:8080], then you can get it to your Nexus 7. This is my favorite way.
By the way, you can't read the ePub books with the built-in reading app (even you can read, you won't like its user experience), so install a 3rd-party reading app is necessary, like Aldiko, Moon+ Reader, etc..