Just like in real life, a CB playing cover 2 or cover 3 does not always stay in the flat from the get-go. He reads the offense and will tentatively follow the WR if he sees nothing coming out of the flat. That's what make those backfield delay routes (the purple ones) so deadly. Because those backs stay in to pass block. The CB playing flat follows the WR, and it's an easy completion and probably 10 yards to the RB. To perfectly illustrate this concept, see Brent Grime's interception vs Brees from a couple years ago. The falcons were playing cover 2 and Grimes followed Henderson since he saw no flats to cover. Brees attempted to fit that ball in that cover 2 gap but Grimes just had an insane vertical.
http://www.youtube.com/watch?v=EvF0Jwfu3hk
On the other hand, if the offense has a RB running a flat or swing as soon as the ball is snapped, the CB will see it (assuming he's not some idiot with low awareness or PRC) and attempt stay in the flat. THAT's when you can exploit that zone gap in cover 2 and burn the defense with a well-timed fade. This is something Madden 15 attempts to fix as opposed to Madden 25, where cover 2 always means big completions because the CB stays in the flat no matter what.
Cover 3 flat, on the other hand, is a tougher problem to solve. Your OLBs and/or strong safety usually as the flat responsibilities, and they are usually the ones with the low zone coverage rating. I get burned more with the flat vs cover 3 in general. But honestly, I'd rather give up the small completions then a big play vs man coverage.