There are SBA loans for small businesses. They benefit non-software companies too - your local McDonald's is probably "government-subsidized" in this sense. The local McDonald's is going to have an easier time getting said loan, but the program is open to any business.

Local and federal governments need developers to write software and will use contractors, but that's not really a subsidy.

The NSF will occasionally fund research that may or may not use software. For example, I see that the Sage math software has a few grants listed:

http://www.sagemath.org/development-ack.html

I don't know that any of this really supports the grandparent's comment, though. McDonald's is closer to being government-subsidized than anything in the software industry.