They work. I've played with so many different QBs (I love drafting QBs) and I could really feel the difference, especially on All-Madden with QB Accuracy down to 6-8, you will have a hard time completing any kind of pass with a rookie with poor accuracy while you can still torch the CPU with Brady or Manning if you get the skills.
The problem is of course, that there's no area in the game where user skill is as important as in throwing the ball. Reading the defense, finding the open man, get the timing right, use the right throw power, aim the ball, all that of course has nothing to do with player ratings, that's all about user skills. But a better QB will have a much higher margin of error on this kind of stuff than a bad one.