Funding
As of May 2012, SpaceX has operated on total funding of approximately one billion dollars in its first ten years of operation. Of this, private equity has provided about $200M, with Musk investing approximately $100M and other investors having put in about $100M. The remainder has come from progress payments on long-term launch contracts and development contracts. NASA has put in about $400-500M of this amount, with most of that as progress payments on launch contracts. SpaceX currently has contracts for 40 launch missions, and each of those contracts provide down payments at contract signing, plus many are paying progress payments as launch vehicle components are built in advance of mission launch, driven in part by US accounting rules for recognizing long-term revenue.
That is not a subsidy, and it’s not going to be ongoing, so it has nothing to do with their launch prices.