Macmillan this definition of make up in Meaning No. 5:
make up [something] to make an amount or a number complete : I'm paying $500, and Dave is making up the difference.
In the dictionary's sentence, suppose we owe someone $700. If I say, "I'm paying $500, and Dave is making up the difference," that means Dave is paying $200.
Now, back to your sentence. Suppose a city needs $1,000,000 for it's annual budget, but sales taxes and property taxes only raise $900,000 in revenue. There's a $100,000 shortfall, and that money has to come from somewhere. Does the city take out a loan? Have a bond issue? Perhaps, but they could also instruct their police force to be more strict about enforcing traffic laws, and issue more fines rather than warnings. That way, additional revenue can be generated to help the city meet its budget.
If this were the case, we could say:
They try to make up in traffic fines what they can't generate in property or sales taxes.
Another way to say the same thing is:
They can't generate enough tax revenue, so they try to make it up in traffic fines.
The way is was written in the news article is not a common English structure, but it's readily understandable by native speakers.