While this is true for shared hosts, if you want to install on your own machine, run test and dev servers (virtualized or no) or cloud-host your app, there is still a very real cost to windows licenses.
The amusing part about the free tools argument is that the cost of tools is such a non-concern in the professional world. I work for large customers on large projects and tools, whether they be Microsoft, Oracle or IBM, no one's worried about that.
Then again, you might be talking about little side projects, my frame of reference is mostly multi-million dollar systems.
Even at large companies, all things being equal, having no licensing costs is a competitive advantage.