While the scope and the barrel may look parallel to each other, they're actually set at a slight angle to one another.

The scope is aligned in such a way that it essentially points horizontally. The barrel, however, is at a slight upward angle. This means the bullet, when fired, will arc upwards and descend in a ballistic arc. With a properly sighted scope, the bullet will intersect the scope's line of sight at known intervals.

This means if your scope is zeroed at 100 yards, and you aim carefully at the center of the target and pull the trigger, the bullet will actually rise until it is close to the line of sight (or above it, depending on the caliber), and then fall the light the target at the point of aim.

It's kind of hard to conceptualize because most arcs we're familiar with are very pronounced. The bullet follows an arc as well but it is very very flat. When you think of the flight path of a bullet in this way, and the scope as a horizontal line, where the two lines (the bullet's path and the scopes line of sight) intersect is where the bullet should go -- assuming the scope and rifle have been sighted to one another.

The handy part about this setup is that the scope can be deliberately adjusted off center by the shooter -- this allows the shooter to compensate for different ranges. If you know for instance, that your bullet drops one inch for every 100 yards it travels (ignore for a moment that this implies a linear path), and you know your target is 600 yards away, you can "misalign" your scope in such a way that it shoots high at 100 yards, but on target at 600. This is what shooters are doing when they're turning the knobs on a scope -- adjusting the crosshairs for both windage and elevation. This way they can put the crosshairs directly on the target instead of having to compensate manually.