I don't have a good explanation for you because I'm simply not experiencing the issue. I have a QB with ratings at or near 90 in SAC and MAC in Tony Romo and I'm just not missing passes (except when I go deep, his DAC is only 76, or when I read the defense wrong and throw picks lol).
I've had missed passes with Brandon Weeden and Dustin Vaughan, but their accuracy ratings collection are all in the 70s. Also played a game with Michael Vick and the Jets once and struggled to complete even 50% of my passes on default All-Pro.
What difficulty are you playing on? Have you adjusted sliders?