It's also longer limbs. The more length you have to control, the more that can go wrong. And big muscles get in the way too. Bigger guys aren't as coordinated as 6' pgs.
And finally, shooting free throws begins with the legs. short guys use their legs to get the ball up in a nice arc. This is why you see guys miss more free throws towards the end of games, as their legs get tired. Big dudes are already up high and so tend not to use their legs as much. They've much flatter shots, especially because they are shooting near even (almost downwards) with the hoop.