OK, I think I see the issue we're running into, after some investigation. Airline Empires appears to use total passenger traffic to rank and list airports, not enplanements.
Differences of a couple thousand here and there are ignored... only focusing on the airports that are significantly off by large percentages.
ATL - Atlanta - should be 89,331,622
ORD - Chicago O'Hare - should be 66,774,738
LAS - Las Vegas - should be 39,757,359
SFO - San Francisco - should be 39,253,999
PHX - Phoenix - should be 38,554,215
CLT - Charlotte - should be 38,254,207
ROA - Roanoke - should be 632,956 - (this is a high priority, because it's currently in-game at well over 5 million!)