I'm been using different variations of Linux for 10-15 years, and there seem like there have been some pretty dramatic improvements over that time. As a server operating system Linux is great, it has many advantages over Windows, but Windows has many advantages over Linux. Both operating systems can be good choices, depending on your needs and requirements.
I'm more interested in the desktop side of things. Linux still hasn't made many inroads on desktops. Many techies have dual boot installations with both Windows and Linux, and some ultra cheap computers come with Linux. Some companies and government institutions have converted wholesale to Linux. But most of these case are the exceptions to the rule. Windows is by far the most popular desktop operating system.
I think that the biggest reason for this is compatibility: all of the applications that people use work on windows, everyone else uses windows, everyone knows windows. Linux has a huge hurdle to overcome to be able to compete like Windows. Even if Linux may be a superior technology and run more efficiently, and even if it's GUI is comparable to the UI on Windows: it doesn't have the same value has Windows.
When you select windows as your operating system you don't have to worry about training, you don't have to worry as much about application incompatibilities, you don't have to worry if your employees will be able to interact with external parties. But with Linux many or all of these can be potential issues that will require time and money to overcome. I don't think that there are any significant flaws in Linux. It isn't perfect, but Windows isn't either. But even with all of the things that Linux has going for it, it doesn't have the momentum to really beat Windows. At least not yet...