When I first started riding last year, my lower back hurt when I went on long rides, though it got stronger and hurt less as I got in better shape. This year, I discovered that my aching back was due to a bad fit on a bike that was too big for me - my back and upper body were too stretched out horizontally, too much "reach". I don't know if you've been properly fitted, but you may want to experiment with moving your saddle forward or using a shorter stem. Hope that helps.