In the late 90's most airline labor had negotiated improved contracts on the heels of the tech boom economy - which later was named the tech bubble burst.
In 2000 the bubble had burst and the economy softened, then came 9/11, and then SARS, and then Desert Storm II (not the video game). All of which caused marked downturns in passenger air travel.
High productions costs (labor, fuel, leases) and no passenger revenue was the recipe for several airlines burning through cash and then declaring bankruptcy. The most notable exception were the cargo carriers, namely UPS and FedEx, who both saw contract improvements during that time frame.