Magic Item Descriptions on Caster Level says
The next item in a notational entry gives the caster level of the item, indicating its relative power. The caster level determines the item's saving throw bonus, as well as range or other level-dependent aspects of the powers of the item (if variable). It also determines the level that must be contended with should the item come under the effect of a dispel magic spell or similar situation.
For potions, scrolls, and wands, the creator can set the caster level of an item at any number high enough to cast the stored spell but not higher than her own caster level. For other magic items, the caster level is determined by the item itself.
So usually the caster level of a magic item is the caster level the magic item uses when the magic item's bearer activates the magic item to generate the magic item's effect. That caster level is usually either at least the minimum caster level needed to cast the spells necessary for the item's creation or set by the game's designers arbitrarily.
In the case of the metamagic rod (quicken), the caster level appears arbitrary as no spells are involved in the rod's creation. Thus the main function of the rod's caster level is resisting attempts to temporarily negate the rod's magic using an effect like the spell dispel magic:
If the object that you target is a magic item, you make a dispel check against the item's caster level (DC = 11 + the item's caster level). If you succeed, all the item's magical properties are suppressed for 1d4 rounds, after which the item recovers its magical properties. A suppressed item becomes nonmagical for the duration of the effect.
The rod's (really high and seemingly arbitrary) caster level therefore lessens the chance of the bearer being put in the embarrassing situation of having spent, like, 20,000 gp on a magic item only to have some level 5 wizard come along and cast dispel magic on it so the metamagic rod (quicken) is just a stick when it's needed most!