I know others have already answered, but I found this learner's diction version of the Merriam-Webster dictionary (and it looks a lot better than their normal site anyway).

http://www.learnersdictionary.com/definition/flush

Scroll down to the 4th listing, which is the adjective version. "even or level with another surface"

So the original poster meant that he thought the card reader should just be completely even or level with the front of the machine. I guess that would just be a plain slot.