Who said anything about a "free" market?
Even in regulated markets, monopolies kill innovation and drive prices up. This has absolutely nothing to do with the free market ideology.
Microsoft has a monopoly in the OS market, used that monopoly to gain monopoly position in the browser market (although they have lost that position over the last couple of years) and a dominant position in the office software market.
Let's see what happened in these three markets.
First of all, the OS. It took MS over 6 years to bring out a new OS. 6 years! Until Windows 95/98, the OS sector was one of the fastest moving sectors around, with plenty of innovation coming out every year, but when MS got to their monopoly position, they have been basically stagnating. Now that Mac OS X and Linux start eating some market share, the development cycle fell from 6 to 3 years!
So, they used that market to get a monopoly in the browsers' market. What happened once they got it? Nothing for 6 years! It was only until Mozilla got a decent market share that Microsoft restarted the development of IE again. And look what happens now, MS will release IE 8 soon, only 3 years after IE 7. Not only this, but since the absolute dominance of IE has declined, we get innovation after innovation in the browsers. Safari, Chrome, Opera and Firefox are all good alternatives that almost monthly release a new faster than ever version racing each other to be the most standards compliant and the fastest.
Office? Again, it was only when Google or Open Office started threatening their market dominance that MS again felt the need to innovate (ribbons, xml file format, Office Live, etc...).
But back to economic theory (I am after all, an economist), innovation creates value, more value means more people can enjoy a decent salary like you said. More people would enjoy a decent salary had Microsoft not taken over those markets because it slowed down the process of value creation! It is exactly BECAUSE an absolutely free market doesn't work efficiently that it should be regulated. Regulation is necessary because left alone, free markets are NOT innovation-optimal. This lack of innovation is what makes communism impossible and why the free market cannot be fully efficient at the same time.
And yes Microsoft force their product onto me (well maybe not me, but the immense majority of PC buyers). Yes you can say public schools are forced onto us, but that is because a private school system is a very bad way to educate the next generation of innovators.
Microsoft doesn't restrict who can program for good reasons (they'd be bankrupt in no time), just like there are good reasons to not allow anyone to be a lawyer or a doctor.
And the taxation bit, well, I have no idea why it is even brought up.
Anyways, innovation is doing more with the same, it is how a society solves the eternal problem of limited resources. Innovation is what should make our kids' world a better world than ours. Having a society that is optimal for innovation is what economics is all about! How our society is able to evolve the best is very complex and filled with needed regulation, but the goal of innovation is crystal clear.
I believe it's time for you to open an economics books before you draw microeconomic conclusions.