It works like this...
MS has grown big, it has eaten into both small and big ISVs, they have the resources and know-how to kill entire industries if they focus their attention to, and the inclination to.
MS has grown big because it let people do what they wanted with the platform (more or less), so it allowed the spawn of the largest ecosystem of software and hardware the IT industry has ever had. They killed most if not all the big players who owned the industry before them.
As everybody points out MS's main bacon is business, essentially AD + Exchange + Windows client, they have such a grip on the market with this combo that they can afford poking a finger on their customers and they ask for more. People is just used to windows and the windows way of thinking.
The only part of the whole ecosystem MS doesn't control completely is 3rd party applications, any vendor with sufficient "push" like google, mozilla can come and build something that runs on windows better than a windows component ie: chrome, firefox.
Suddenly all this work of producing a cohesive end-to-end business environment (or one that MS can control) is gone. You do not need IE anymore, loses the grip on the most desirable tech ever... the internet.
How do they prevent this? well, Apple had a nice idea with their wallet garden, and a brilliant implementation: Their APP store, if they were to produce one for Windows, they can A) close the door to 3rd parties disrupting their environment, b) get even more money c) Control the main or universal windows communication mecanism, your windows screen to push MS messages, ads, etc. d) offer to the windows-addicted masses even more control over the application delivery mecanisms, eventualy disabling the ability of the user to install software locally if not via the windows app store, esentially reducing the likelyhood of getting viruses or unsactioned apps.
Resuming, this is all part of a 10 year plan to transform the windows ecosystem into something were no-one else but Microsoft can tell what to run where and how much you have to pay.
If you're an ISV and want to play ball on Windows, you complay and pay your share to MS, if your app proves to be popular, or you discover a profitability niche, Microsoft will have that information on their database, and who knows they could even use it to their advantage.
People, the PC platform is only good if open, if turned into a walled garden the PC is nothing more than a remote terminal, a sort of distributed mainframe always dependant on the mothership.
And the reason this is happening is because MS as a business runs on what Gates and Ballmer learn during the 80's if you let competition thrive eventually you wither away because somebody else will come with the next best thing.
You have to realise that there are a lot of penguins out there, some are very clumsy, some are doing nice tricks, they are evolving at a fast rabid pace, most of the time for free (It has a cost I know), eventually one of them will become popular, and we do not want people to discover that it is good enough.