Government contract is not a subsidy. It's a payment for a product or service provided to the government. Examples of subsidies are section 8 housing or USDA PLC. SpaceX providing launch services to the government is nothing like that.
Distinction without a difference as it pertains to the conversation. Most of the money SpaceX received from the government was under the COTS program where NASA gave SpaceX money to develop a product and then NASA would become a customer of that product. It is as close as you can get to a technical subsidy without it being technically a subsidy.