Yep, I learned this 7 years ago when I was given custom orthotics in a heavily structured shoe and everything just got worse. I too gave up running (for cycling, yay!) until I read Born to Run last fall.

I'm now running again, injury/pain free and my milage and speed is increasing steadily. I run either barefoot or in a pair of 'BarefootTechnology' shoes.

And I would also like to add that I have virtually flat feet and I over-pronate. My podiatrist said 'so what? That's how your particular foot works, don't fight it'. Smart man.