This has nothing to do with route running, but everything to do with Maddens poor representation of passing. Regardless of your receivers ratings, if you throw the ball too early on, say, an out route, the AI will think it's a fly/go route.
Route running isn't programmed into the engine, only changes in direction are. So if you throw before a receiver has changed his direction, then the system believes he's running a different route. And as long as players in Madden are psychic it doesn't really matter when you throw it. All players, defense or offense, instantly reacts to where the ball is headed.
In short, route running is basically just a rating that allows separation against the man coverage rating. If route running is higher than man coverage, then the receiver gets a speed burst and thus separation from the defender. If the man coverage rating is higher, then the defender gets the speed burst (and sometimes even run the remainder of the route ahead of the receiver).