Usually hand-drawn/painted illustrations aren't going to have a single shade of a particular color, even if you used a single color to draw it. That's because there's texture to the paper, to the pen/paintbrush, and there's usually variation in the amount of ink or paint deposited on different parts of the paper. The scanning process itself can also introduce noise, but even with the best scanners, you still won't get solid perfectly uniform colors.
That's why digitizing an illustration is a manual and often very laborious process.
If you have a digitizing tablet, this can greatly speed things up. You can either import the image into Photoshop and digitize it as a raster illustration, or you can import it into Illustrator and make it a vector illustration. It largely depends on your preferences and the style of illustration.
If you're lucky, and you have a very high quality/high resolution scan and an appropriate design, you can use Illustrator's live trace feature to convert your image into vectors for you. This process works better for some images than others. If you just have solid, well-defined regions of color (no gradients) and not too many small details, then this method works very well and requires very little manual tweaking afterwards.
In Photoshop, you can use the magnetic lasso tool to manually select each color region and fill it with a single color (preferably as a new fill layer). Or you could just use the paintbrush tool and eraser and re-create the illustration.
In Photoshop you can also select a color range, but that doesn't work too well in my experience (especially compared to the color range selection in the HSL dialog).
Because it's such a tedious process, I think most illustrators prefer to just sketch the outlines on paper; scan it; and then do the inking and coloring digitally.