I thought this was a common misconception.
While sometimes people are limited in their squat by flexibility issues much more often they are limited by their inability to recruit things properly. They lack motor control of the pelvis.
Check out Ripptoe's article (this site) 'proper back position for power'.
Use his diagnostic tests. Vid yourself side on if possible. Are you able to hold a lumbar arch at all? It is possible that you simply don't appreciate how you need to hold yourself in the first place. Once you have the general idea of it then you will get more mobile (movement with proper recruitment) by... Squatting.