I am making approximately 25% profit. There are no secrets--you just have to be patient and disciplined. The first pillar of success is aircraft choice. Availability shouldn't be the only factor in picking what aircraft you want to fly. I have only one competitor at my base and my entire fleet is brand new BAC 1-11 500's--I ordered every single one directly from the manufacturer and had to wait. My competitor has dirty old 720B's that carry around 40 more pax than my 100 seaters, but also burn 5x the fuel and are older with increased maintenance costs. Needless to say, I don't think he'll be surviving too much longer.
A way for a newer player to learn the ropes is to base at a secondary airport that doesn't have any other airlines based there. If you are at a smaller regional airport in the states you can focus on dominating the routes to the major hubs. For example, there is no one based at AVL and there are only 2 flights/day into the airport. If you were to base there, the top 5 airports have approx ~150pax/day demand and if you use prop planes that aren't fuel hogs, you can dominate those routes with frequency and turn a healthy profit by controlling your costs and flying your planes 80% full instead of 50% full. Once you've dominated all the routes worth flying out of AVL, you could open a second base and do it all over again, but in the mean time--pay attention to what is going on. I've been playing this game for over a year and I still watch things like a hawk because it can be very easy to lose money if you aren't paying attention. If there is a route that can support more than 1 flight/day, I don't fly it unless I can dominate it. There is no use in flying 1 flight to Atlanta when you're competing against 10 other flights/day--you won't turn a profit. Airlines at the big airports like Atlanta aren't going to waste precious resources on trying to dominate a route like ATL-AVL, so you'd be in a good place. Furthermore, if you are flying 3x daily from AVL-ATL with 50 seaters and you're competition is flying 3x daily with 150 seaters--you'll still have higher load factors as passengers prefer smaller planes.
I just use AVL as an example--there are plenty of other smaller airports you can dominate as well (look at airport info before you bankrupt and you can check demand levels before basing there). If you are trying to compete with the big boys and you're still a newbie, you're going to lose and lose big. You're not going to understand that you need cash for C/D checks or how to manage a fleet successfully until you can master the fundamentals.