As I recall they make money on Orbitz' affiliate program.
According to an Oct 2010 article by TechCrunch [2] "Orbitz pays Hipmunk the standard rate of $3 per flight sold". Hopefully they did some renegotiations recently or have some other contract in place that generates Hipmunk more income.
[1] http://replicatorinc.com/blog/2010/11/alexis-ohanian-hipmunk...
[2] http://techcrunch.com/2010/10/06/how-hipmunk-almost-became-b...