Waste can cause these stains if you are not diligent about regular cleanings. Such things build up over time, especially if you are conserving water and not flushing after each use.  However, this is seldom the cause. The brown stain in the toilet bowl usually comes from hard, mineral-rich water—the minerals have calcium compounds, iron, and manganese. Iron oxide, also known as rust, is the main reason your toilet has stubborn brown stains.