Okay, there's a mixture of good and bad advice in that single reply. While I realize that Michael may no longer be playing after so long, I'm sure there are others with similar issues, so I will share what I've learned from slowly clawing my way out of the hole:
1) Be careful with your choice of planes. I'm not familiar with the Fokker aircraft mentioned in the original post, but I strongly recommend sticking to turboprops until your airline is firmly in the black. Props are generally cheaper to operate than jets, so unless distance or passenger load force you to go to jets you should stick to props.
2) ADVERTISE your routes. Routes with an active ad campaign have much higher load factors and make more money as a result. The trick is, AVOID radio and TV advertising until, again, your airline is operating at a profit. Radio and TV are horridly expensive: marketing costs alone forced my one reset this game because I didn't realize that yet. Steer clear until you can afford them.
3) Here I do agree with Sigma. KEEP YOUR PLANES IN THE AIR!! Every minute they're not down for A/B maintenance, they should be flying and making money. Planes COST MONEY sitting on the ground!
4) HIRE ENOUGH PEOPLE to do the job. Don't over-hire: personnel costs can break an airline in a hurry if you go overboard. But by the same token, UNDER-hiring costs you in terms of both image AND MONEY, because lack of staff can force delays and/or cancellations. Keep ALL staff areas at 100%, perhaps slightly over in Ground Handling, customer relations and MAINTENANCE.
5) PRICES. Always set the initial price for a given route slightly below the default value, and always make sure the price ends with a 5 or 9 (125, 179, 499, etc.). Customers think they're saving money that way and will fly your routes more often. You can always raise prices later to increase profits, but never go so high that your load values drop more than 3-4%, and always remember the 5-or-9 rule.
6) ROUTES. Anchor your airline with high-demand routes (ex.: New York-Los Angeles) that will carry consistently high load factors, then add other routes as profit margins allow. Assign routes to aircraft large enough to carry the expected load, but not so large that they consistently fly with empty seats. Planes burn fuel, bigger planes burn more fuel, and fuel costs money. Keep your costs down.
I'm sure there's plenty more, but that's all I can think of at 7am lol. Clear skies!