Many people don't buy traditional PCs at all anymore. My new girlfriend has a Macbook Pro and shes never going back to a desktop. That's a bunch of market share they can't chase unless they get into OSX and Linux ports. Valve is smart, like you said they are slowly creating a viable alternative to Windows gaming. There are already 1200+ games that we didn't have a year ago. That number will keep growing. As it grows so will attention to drivers from Nvidia and AMD which will help out the transition significantly.
PC gaming is supposed to be about choice and options. The idiotic attitude where you should only use one OS is borne from fear of change. Stuff like this is only good for consumers in general and that's all it is, an option.
The worst case scenario for Valve is a total shift to mobile platforms. Microsoft isn't doing itself any favors on the PC so that's not a real concern, they are so desperate to convert people to Windows 10 that they're trying to force it on them through Windows Update. Mobile is the real threat now, many publishers can't ignore that revenue stream from shitty IAP games.