Flying props, especially small ones, is always a challenge in airwaysim. The displayed weekls profit is "profit after direct costs deduction" (ADCD profit). As Sigma explained, they lack the overhead costs of the company. In order to maintain an effective cash flow profit with these routes and planes, you should reach a weekly profit of around 100k USD with a 48 seater plane. That is based on est. 100,000 USD monthly lease fees. With smaller planes, as a rule of thumb, you can take the same basis and simply lower the lease costs accordingly. With an EMB-120 you will have est. 25,000 USD less in leasing fees per months, bringing your cash break even down to somewhere at around 80,000 USD per week, due to lower directs costs, route fees, etc. but also the plane itself.
You usually reach this by having your plane in the air a lot. Flying routes up to 300nm from your hub is one option. If destinations are further, you may try flying ABCBA-routes instead of AB-routes. However, it is much more difficult with small a/c like the EMB-120 than with the DHC-7 or the HS748 etc. If you succeed to fly four destinations per day from your hub with one a/c, you should be able to make a cash effective profit.
Other factors also impact significantly. Fuel prices can be felt at these thin margins very quickly. Take a look at the pikes in fuel prices during the last 12 game months.