As a result, almost half of the $96 million spent since fiscal 2007 has gone toward administrative costs, federal fines or keeping projects moving after the city lost state and federal grants. For the last few years, the money even has been used to pay rent for the housing department's offices.
Not half of the money collected (130 million). Half of the money spent (96 million divided by 2). The article doesn't specify the proportion in the four items it listed, as well.
Very clearly, this type of thing means that money is still in a pile somewhere not helping people with housing (probably earning interest, though, and funding other stuff/people)
It was the Houston Chronicle's repeated questions about financial discrepancies that led the city to discover $46 million was available for new projects, tens of millions more than officials thought.
They had more money than they though, as well.
So, the overall take from this article is that Houston has more money than it expected. It isn't using it because it sucks at record keeping.