Here's my opinion - search on "stroke instructor challenge" if you want more info. It's physically possible for your cue to move straight but it is not physically possible for you to stroke straight. Someone else mentioned timing - your cue is essentially moving in an arc and you're either fighting it or trying to hit the ball in the small window when it's moving "straight".
Having your elbow and shoulder in a perfect line with the cue has a similar but less pronounced effect. Using a pendulum instead of piston style stroke does nothing to address the actual problem of the stroke being out of line.