I've taken a look at your airline and your base airport and I see a number of problems that contribute to your difficulties.
First up, 3 aircraft is not usually enough to cover your operating expenses and have any profit left over. It's important to grow to a bit bigger size quickly, so that the monthly leasing costs don't catch up to you (you pre-pay 4 months when you lease an aircraft) before you make enough to cover them + pay the staff.
This immediately leads into the second issue, that the DC-9 is really way too much airplane for CTU in DOTM. CTU is a 90% domestic airport, and there are only 5 airports with enough demand to support a DC-9-30. Looking at the demand, something in the 40-50 seat range would seem like a better choice.
The third thing I see are those DC-9-10s. They're old birds, so they cost a lot more to maintain. Also, they consume ~20% more fuel per/passenger/hour than the DC-9-30. They can still make money, especially on short legs, but they will make a lot less money than the DC-9-30.
If you want to retry at CTU I would suggest using something like the F.27. There are some available used, and you can order new as well. If you'd like to operate DC-9s or similar sized aircraft, however, you probably need to find an airport with a bit more demand.
I hope this was/is helpful.
edit: I was assuming that you're already in negative cash between your company value and your comments here, if I'm wrong about that let me know and I'll see if I can come up with any ideas to help you recover this airline