In addition to nolonarnolonar's excellent answeranswer.
There are tons of raw diamonds on Mother Base that your soldiers keep hidden for themselves. CQC and interrogate your own soldiers (on any platform but the command ones) and they will reveal the locations of said diamonds. You can then collect them. Also, all the diamond re-spawn every three main missions you do thus allowing you (with some grind) to get a lot of money for nothing. Note that as a side effect, the moral will grow since you are teaching them CQC moves.
Second, you can sell resources. Some plants are worth a fortune and a quick trip into the field with D-Dog will replenish a lot of them. Vehicles are worth selling as well as long as you keep 2-3 of each. Finally, other resources (such as "precious metal") can be sold but be careful as this might limit what you can build.
This is by far the simplest way to get lots of funds if you are in the red.