The big firms like JP Morgan, RBC, Bank of New York Mellon, etc. use subsidary clearing firms but there are huge firewalls and regulatory restrictions on interactions. Those companies are able to formulate their own clearing houses because they do trillions in asset trades across the globe.
Companies like Zecco and TradeKing and many of the other discount brokers don't have the volume to do so, and the cost to set up an subsidary with duplicative management and staff would be prohibitive. It's simple economies of scale at work.