There are many beginners guides for different purposes, like
http://linuxcommand.org/index.php for a first insight in using the shell.
The best way to learn Linux, IMHO, is to install one and then have a look at the documentation for that distribution, so that you first learn the basic things, like installing software, playing with the different graphical environments, ... .
Once you have done that just pick yourself a topic (if you are somewhat experienced in programming shell scripting may be a good start) and learn about it. Most important: Forget the Windows way to do things.
There are two important questions that have to be solved for a successful start into Linux:
1. Which distribution will you use?
2. Which graphical environment (if any) will you use?
For 1.: The distributions mainly differ in two things:
a) The package management systems. Unlike in Windows, in Linux programs are installed using a central instance, the package management system. For almost any distro (there are of course exceptions) are different interfaces (or package managers) for that package management system available, for example in Debian you can use apt-get on the command-line and Synaptic in the GUI.
b) There main goal: There are distros that are aimed at new users and users that want to do anything in a GUI, like Ubuntu, Mint, Mepis or PCLinuxOS. There are also distros aimed at server usage, old hardware, being cutting-edge, being rock-solid, ... . These differences also cause that different distributions are perceived to have different "difficulty grades". For example, a distribution like Slackware, where almost all system configuration is done on the command-line is perceived by many people to be more difficult than a distribution that has a GUI dialog for everything. If that is really so depends solely on the user. I, for example (and I know I am not alone) prefer to use the command-line for configuration, in my eyes it is much simpler, more consistent and the to the point than clicking through a GUI interface, but as stated, other users may prefer it in a different way.
Having said that, the only way for you to find out what you prefer is to try a few distributions and see which way you like.
For 2.: Unlike Windows, in Linux the core system and the graphical environment are separated.
Linux has several complete desktop environments (DEs), that come with the basic tools you expect from a system, like text editor, calculator, browser, ... . The most common are Unity, Gnome, KDE and XFCE. There are also some newer ones, like LXDE and Razor-Qt that may not be so stable and feature rich like the bigger ones.
Also available are the window managers (WMs), they come with nothing but the ability to decorate and handle your windows, but most of them are very configurable and easily extensible. This way you can assemble your own DE with a WM as base and your favorite software on top of it. The most common are the Boxes (Fluxbox, Openbox, Blackbox), Enlightenment, FVWM, WindowMaker, ... . There are also a bunch of tiling WMs (containing my facorite WM, wmii). To have a a first insight how all of those GUIs
can look (most of them are highly customizable) just have a look in the
screenshot section of LQ.
Which GUI you choose is dependent on two factors: Of course your personal taste, if you are a fan of eye-candy better go with KDE for example, and second your hardware specs. The "bigger" DEs (Unity, Gnome, KDE) are quite demanding when it comes to hardware resources and they may be quite slow on older machines, while the WMs will run on almost anything that can display graphics.
If you have a decent machine the same applies to GUIs as applies to distros: Just try them and see what works.
I hope that helps to get your first steps in Linux as trouble free as possible, have fun with it.
