You're assuming they pay $100 for a Windows License. Or that building, validating, and supporting a Linux image would be cheaper in the long run than installing Windows and maintaining a few drivers.
And that's not even taking into account the market demand for such a thing which is negligible.
I've heard OEMs make more money from pre-installing adware/spyware/trialware than what they pay for the Windows license.
You can always decline the EULA and try to get a refund for the bundled Windows license. In Europe it is supposedly easy to get a refund due to a European Union directive on unfair commercial practices: http://no.more.racketware.info/en/europe
Is that a troll? Linux has tons of native applications in just about every category. It is absolutely packed with alternatives. I don't use Linux daily anymore, but I almost never had an issue finding programs for what ever task I wanted to accomplish. More often then not the problem was a glut of choices.
Yes lots of alternatives, you can argue that there is an alternative for virtually everything that is available if you are willing and know how to find it.
This is the same argument that Windows Phone (ironically) make, but most people want the same programs that all of their friends run. Computers and most other electronics are appliances to most people they just want them to work without any thought.
It is fair to say that certain software doesn't run (or run well) on Linux. It is also fair to say that most people don't want to learn how to use new software especially when they already know something else that works.
I think however, it is misleading at best to say that it doesn't have many native apps.