I'm not sure what alternative the author has in mind. Should the TSA separately bag the 47 cents you left in the plastic bin with the day and time it was lost, so that it can be returned to you in case you decide to come back and claim it? That's just not realistic.
They basically have two choices: keep it or throw it out. And why would you throw out money?
TSA keeps the spare change left in security bins, which amounts to $3m over unspecified number of years, with "some evidence that in 2013, TSA was scrounging about half a million dollars a year from security bins" without actually pointing to any evidence. Author finds this a big deal.
It's not linked in the article, but the number comes from a committee report [1] related to the TSA Loose Change Act (which _is_ linked in the article, but finding the report from that link is indeed nontrivial).
I think the interesting part is that TSA keeps the money to fund its own operations. The actual amount they raise is not too surprising.
They basically have two choices: keep it or throw it out. And why would you throw out money?