A primary source of roof leaks doesn't actually invovle the roof covering but the flashing. Unfortunately, flashing is one of the easiest items on the roof to incorrectly install. It's not that the parts are that complex - they're not. The manufacturers have made them easy to install. And, properly installed, the flashing is nearly leak-proof when installed on a simple roof.
However, there are very few simple roofs. Examples of simple roofs are dog houses and small outdoor sheds. Rarely will you find a plumbing vent stack, chimney, fan vent, valley, side wall projecting above the roof, etc. on a dog house. Most of these are common on a typical home.
The easiest way to think of flashings is to consider them the transition from the roofing materials (shingles, for example) and projections (i.e, a chimney.) Many people expect roofs to perform for a minimum of 15 to 20 years. Some roofs can be expected to last 50 to 80 years. This means that the materials which are used for flashings must have the same, or greater, life span as the roofing material itself. Copper, tin coated steel, lead and galvanized steel are examples of traditional flashing materials.