What is the difference between taxonomy and navigation of a website
and what are content relationship maps of a website?

taxonomy: the classification / category / group of contents. it can be
single or in hierarchical format. For example: computer,
computer-internet, computer-programming, computer-programming-c++

navigation: shows you path to the contents of your web site. pretty
much like site map.

content relationship maps: the relationship between contents. this can
often be achieved by specifying related keywords when you create a
content. A document is said to be mapped to all the contents with the
similar keywords.

If possible, download drupal from www.drupal.org. It is one of the
content management system that employs these terminologies.