ok... let me explain this visually and it will make all the sense in the world.. but i do want to clear something up from the get go A BULLET DOES NOT RISE COMING OUT OF THE GUN!!!! physics doesn't allow that one to happen... yes the bullet begins to arc as soon as it leaves the barrel due to gravity but it never rises!!!
in the first diagram.. this would be if a shooter was shooting a gun with a scope.. the scope perfectly level with the world as well as the gun barrel perfectly level with the world... the bullet and the line of sight would never interesect because gravity is causing the bullet to drop and due to the offset of the scope (height) and the barrel these two obects can not cross no matter what.

the second diagram shows what is truely going on and where the misconception of a "bullet rises" out of the barrel comes from...

as you see when you adjust your line of sight (zeroing in a scope at x distance) you are actucally adjusting your line of sight in minute measurements to get your line of sight and the bullet trajectory to cross.. now depending your guns ballistic trajectory and where you zero it in (say 50 yards) it could be high at 100 yards as the image dictates. BTW those ore the exact same arcs one is just rotated. obviously the gun angle and line of sight are overly exaggerated to show whats going on. now it makes sense visually huh??