The MM makes $ in many ways. Also, this could be order flow from an Agency Trader. I am sure you have not heard of that. The MM can make $$$ via the spread, especially with pinks with 50% mark ups. Knight is notorious for paying for order flow from agencies. Also agency firms have many ways to charge fees, not $5 per order.
I spent years as an licensed professional Agency Trader, I managed ACTing my trades, clearing my trades, clearing my blotters and managing my accounting, with help from software.