Is $1000 the so-called rack air-rate? ie. the rate by which airlines post as their maximum rate for minimal lead time booking?
If so I suspect the rates by which airlines charge teams are calculated at various discount schedules, especially if one airline is granted the right to be the official CFL carrier.
CFL teams (and the league) employ travel planners amongst their office staff. These folks are charged with arranging flights, hotels, food services and other ancillary services teams require. So I suspect most air tickets are discounted anywhere from 15% to 40% depending on lead time provided and expected payment time on invoices (ie. 5 days, 30 days, 60 days, etc.). Same principle holds for hotel rooms. In fact many teams will shop for hotels that are willing to contra (aka trade) hotel space for promotion on the team's radio broadcasts, team programs, home game announcements, etc.