The money is presumably to cover the cost of sending someone out to find the accused and drag them to the courthouse. If someone can't afford to pay the bond and then tries to run, I don't see how that money can be reclaimed except for the taxpayer covering it.
Someone has decided it is easier to simply keep the accused in jail. Assuming they've done the math on costs properly it would make sense. Taxpayers shouldn't be in a position to cover the cost of people running from the law.
It is an uncomfortable system that clearly biases in favour of the rich - but the rich are the ones covering the cost of it all so I am comfortable standing up and saying I don't mind if they get special treatment. Wealthy people pay something like half the taxes; it seems reasonable that they can wait for their day in court in comfort. Wealth comes with privileges and they aren't criminals until they are convicted.