Compared to Windows, GNU/Linux is a far more diverse operating system. Because no one organization builds it, it has more than one way of doing things. Because its developers are highly individualistic, they provide the means for users to do things their own way.
The result is that, unlike Windows, GNU/Linux has more than one distribution, more than one desktop, and more than one of just about everything. That's what its users prefer.
Granted, the options -- to say nothing of their names or acronyms -- can be confusing to a newcomer. However, much of the confusion is due simply to the contrast to Windows. From an end-user's perspective, the differences between the most popular distributions are not that great.
Five minutes' research will identify the likeliest choices, and in every case you can get through an installation with a minimum of decisions and help for the few that you do have to make. Once you are running the distribution, you can take advantage of all the options to create a highly customized desktop, but you can be reasonably content with the defaults and maybe changing the wallpaper.
In other words, the options are for experienced users. Newcomers can ignore as many of them as they choose.
You hear this myth in two forms. In the first, the complainer talks about compiling from source code. (What is hard about uncompressing a file then following the standard instructions to run the commands configure, make, and make install is beyond me, but let's accept that many people find the unknown intimidating). In the second, the complaint is that you generally can't go to a hardware or software vendor's site and download and run a binary to install, like you can on Windows.
People who make either of these complaints have missed the fact that GNU/Linux does things differently. Each distribution maintains its own repositories of software, all packaged to run with it. Unless you know what you're doing, you confine yourself to software in this repository, using a graphic tool to install, or its command-line backend.
When you stick to your distribution's repositories, software installation on GNU/Linux is actually far easier than under Windows. You don't need to go to the store, because all the available software is available online. You don't need to pay for it, or register and activate it, either.
If you suddenly need new software for a task, you can locate and install it in a matter of minutes. If you want to browse several alternatives, you can do that, too. All you need to do to enjoy these conveniences is learn a little bit about the operating system instead of barging ahead and relying on hearsay or your old way of doing things.
Such arguments say more about those who make them than about GNU/Linux. At worst, they show an unfamiliarity with the current state of GNU/Linux, and at best a collection of habits and prejudices.
So what are the real reasons that GNU/Linux is not more popular? The old standby argument about monopoly is probably a main reason. When Windows comes pre-installed on most computers and you have to search for GNU/Linux pre-installs, the problem seems self-evident.
Still, the resurgence of Apple in the last five years suggests that the monopoly is not absolute. An even simpler explanation is that, despite their complaints, most people are familiar with Windows and unaware of GNU/Linux or any other alternative. They lack hands-on experience, and rely on hearsay and third hand accounts that they have no way to evaluate.
The excuses they make for not using GNU/Linux reveal this lack of familiarity very clearly. People may be saying that GNU/Linux is not ready for them, but the inaccuracy of their excuses suggests that the real reason is that they are not ready for GNU/Linux.