A couple things probably play into that which doesn't get talked about a lot.... angle of attack (AoA), and the roll radius of the face. If one has a really positive angle of attack with the driver (say a 9* driver for example), and impacts a ball that is teed up high with a high AoA, and lets say hits it above the middle of the face (depending on the actual roll radius, loft toward the top of the face could be around 11*-12*), it's easy to see how people with a low lofted driver think they need to go with a lower lofted driver to get their ball flight down.
People with a sweeping driver swing, or even a negative angle of attack will almost always do better more loft. Tiger's current driver is...... 11.25*!
I think people sometimes don't take into account the AoA and the roll radius of the face of their driver, and jump to the shaft as the root of their height/trajectory issues. The thing about the roll radius is (using a driver measured at an actual 10* as an example again), depending on the radius, the driver could be 10* at the dead center of the face, 7*-8* towards the bottom, and 12*-13* towards the top. Now factor in a manufacturing tolerance that is almost always at +/- 1*, and that "advertised" 10* driver can have a face with loft ranging from 6* to 14* depending where on the face the ball is struck. I've even heard many stories of Ping drivers measuring 2*-3* higher of actual center of face loft than what is on the sole. I've also heard that it might be done on purpose..... but I'm not going there!
As far as the shaft flexing enough at impact to add a little extra loft... if you have an early or even maybe a mid release, you have already thrown out the power, or lag, and the shaft wont do much for you then. If you have a mid to late release of the lag, then the shaft definitely comes into play.
Johnclayton - I'm guessing that you have a negative angle of attack?