First, Microsoft has had to play pretty carefully in the past decade to make sure that they don't draw any more antitrust ire.
The other thing would be that they don't have to manipulate the market forever, just long enough to lock out competition.
A perfect example of this in the tech world would be Intel.
They did everything they could to keep AMD locked out of vendors like Dell for years, even when AMD had a superior product. Fast forward a few years, and not only is Intel still the dominate player in the market, but their lead in process technology makes it extremely difficult if not impossible for anyone else to compete. For example, Ivy Bridge has a slightly higher transistor count than AMD's Bulldozer, but has a die roughly half the size of the AMD part.[1] That means that even if AMD was producing a part that performs competitively with Intel, they're going to have difficulty competing with them on price since Intel can crank out more dies per wafer.
Obviously it's entirely speculative whether AMD would have been able to capitalize on increased market share and keep up with Intel long term but Intel doesn't really need to manipulate the market like they used to anymore since they've managed to put themselves in such a comfortably entrenched position.
[1] - http://www.anandtech.com/show/5771/the-intel-ivy-bridge-core...