You´d have to do a lot of pointless flights in order to be really broke. You can always go back and reload and there is a way (though it´s a bit complicated) to make an infinite amount of money (just let get yourself abuducted in the Bermunda Triangle investigate the alien spaceship thoroughly and BOOM all your money problems will be solved!)
There will also come a point when you don´t have to fly at all anymore. Letting yourself get caught by the alien persuers also saves travel money.
It also helps that Annie (who has far less money and also cannot make any like Zak) is only needed in three (maximum two) places in the whole game though and you can even let Zak pay for her bus ride and first plane ticket!
Once you got these basics down and you have an idea what to do the order doesn´t matter anymore, but never leave a place when you haven´t looked for absolutly everything there.
You can do it!