It is really silly to compare the two.

I have a duplex as a rental property. I make about $300 on each unit totaling $600 per month, or $7200 per year. Big Shot Apartment Company Llc owns a 100 unit buildig and only makes $150 per month on each unit. Am I twice as profitable as them because I am pulling down $300 for each unit? They make $15k per month and $180k per year...

AA could probably cut the 1/3 least profitable routes, and have the same profit margin as Spirit. As Spirit grows, they will put the aircraft on the routes that will be most profitable. Eventually the most profitable route may only draw a 3% profit margin. 3% is still a profit! If you have 100 of those it adds up to a lot of money.

The other thing to think about is: Spirit may be able to make a 3% margin on routes where AA loses money.

Point is: There are a lot of things to consider when comparing the financials of the two..