Typically because the arrow/bolt is traveling slower. Bulletproof glass is often set up to intercept high velocity, low mass objects (i.e. 0.2 oz of lead) not slow velocity high mass objects (i.e. 4 oz. of wood and steel).
Also because a bow with the right tip focusses all of it's power into a MUCH smaller area, than a bullet does - small enough that for woven / fiber based materials, the top my actually pass BETWEEN strands, letting the rest of the arrow-head part the material, instead of having to actually break it. (Plus, the sides may actually be blades, further reducing the efficacy of stuff like kevlar).