Yeah! Some good things about using the pencil tool:
1) It is easy to clean up your lines using either the pencil eraser or the pencil with white "ink". Lines made with a brush are harder to clean up because you have to try to match the antialiasing and opacity blends.
2) pretty easy to fill color areas with the pain bucket (if you enclose most of your areas with unbroken pencil lines).
3) always delivers sharp crisp lines. If you want to soften them, you can apply a slight blur or median effect later.
I use the pencil tool and then flatten and reduce size of image before saving for web. If you work at about twice the final size or larger and then reduce the finished art it stays sharp with out looking pixelated.