There are plenty of reasons... they're not necessarily good reasons, or reasons I agree with, but the choice always lies with the end user.
Some people just don't want to go through the "hassle" (despite how trivially simple the process seems to anyone on these boards), and there will always be a stigma attached to 'iffy' romsites that may put off parents from allowing their child to utilise cfw.
With CFW, you can do much more with your system than if it was just plain stock, the ability to backup/swap saves with Checkpoint is alone worth it for me, running Out-of-region games and VC injects are great additions as well. So yeah it's worth it!
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