I have also wondered why I should build up my stomach muscles even though I have a huge layer of fat covering them but there are some great side effects:

As Nat said, it is awesome for your back, but it also does this:
I'm not sire if you have this problem, but my mom calls it a "butt in the front" (the area below the belly button, where your stomach kinds of bubbles out, I think this mainly effects women that have had children, however I have one and I have no children )...well if you do exercises strengthening that area (lower-abdominals), it pulls the "butt in the front" in. This also makes your posture look much better too