Damn it, I thought this thread was about joey.
I'd like a bit of clarification, do you mean your skin hurts or the joints at the base of your spine are bothering you?
If its the skin then you could have two problems: one you are working an too hard a surface and your tailbone is rubbing against the floor, two you are using momentum to do your situps (jerking head and shoulders forward). The momentum thing is suprisingly common and could easily lead to a neck or lower back injury.
If your spine hurts then it sounds like you are using your hip-flexors too much and they are compressing your spine, look into other exercises that don't agravate your back.