Because it is a measure of comparative business activity that does not vary with exchange rates or ticket prices.
Fleet size tells you very little. For example is an airline that operates 20 31 seat DO328s "larger" than an airline that operates 15 469 seat A380s?
Number of passengers is also not truly indicative of operational size. Is an airline that carries 1 million passengers a year between LHR
really "bigger" than an airline that carries 750,000 passengers a year between LHR
If you are trying to compare economic activity theoretically the best measure is revenue. But airlines can slide up and down a revenue ranking list for no other reason than changes in relative exchange rates. So, for example a non-American airline could show 10 per cent growth in RPKs while maintaining ticket prices but because its home market currency lost 15 per cent of its value against the US $, comparative revenue figures would show a decline.
RPK does not have the intrinsic problems of comparison that many other possible measures have.