There are several fantastic books that have been released on an open or creative commons licence and will give you a really good understanding of Linux and its
filesystem- they are so good that I have never needed to buy a textbook:
For Ubuntu, you could start with the Ubuntu manual, which is bang up to date for 12.04. The Ubuntu pocket guide is useful for general concepts and principles, but does not cover more recent versions of Ubuntu from the last few years.
However, for a deep understanding of the
package management and
administration, the Debian Handbook is incredibly detailed and interesting, as Ubuntu is based on Debian.
In Unix as a whole, it is often said that everything is a file,and an older book such as Rute explains this well. It is well respected as a good Linux textbook and contains a full copy of the official specification of the
Linux Filesystem Hierarchy. However, while that section is still very relevant, the book as a whole has not been updated since 2001, so it is best to use it for background information, and always refer to Ubuntu practice before copying any commands from there.
For Linux and the command line, I have learned a huge amount from this book; it is extremely well written and gives clear examples when explaining any difficult concepts. It really explains how Linux, its filesystem, and tools fit together. It is definitely worth reading all 500 pages plus!
A standalone copy of the official filesystem specification (2004) is available at the Linux Documentation Project, and this tutorial and summary also goes into some relevant general detail.
man hier in your terminal will give you a valuable summary of the
filesystem hierarchy and is indeed a very useful basic reference guide that comes in handy when you want to quickly look up various aspects of the hierarchy.