Answering this question really requires a bit of explanation on the linux, or rather, unix file structure. If you want to really understand this topic, read the documentation for the File System Hierarchy Standard: http://www.pathname.com/fhs/
This is the same document used by Fedora package maintainers when they determine where their packages should install files.
Here's my very basic summary of the document, for a windows user:
Basicly, files are stored by their function. This means files are stored in folders indicating what function the file has, rather than what piece of software it belongs to.
Unlike Windows, unix systems like Linux (Fedora is a Linux system), doesn't use the C: drive, D: drive and so forth system for displaying the information on the hard drives. Instead, it uses one root which contains everything on the computer. In the root there are several standard directories, which contains files which serve a certain function. If you wonder why this is so, read up on the history of UNIX. Some examples:
/boot contains files used to boot the system, and only files used to boot the system.
/home contains folders which acts as each users home dir. This is the only directory a user should have write access to, IE: This is where all files, documents, music, movies, user specific settings and so forth are stored.
/etc contains system wide configuration files. Settings for the entire system.
/usr contains sharable, read-only data. This folder has it's one hierarchy and this is where the binary files, the libraries and the documentation is stored, in short, this is where applications are stored. Run-able files in /usr/bin, libaries in /usr/lib and documentation in /usr/share/doc. The /usr/ hierarchy is a bit complex and I won't go into it here. See the FHS for details.
You then use a package maintainer solution, Fedora uses RPM, to keep track of the system files. The end result is a system where you really don't have to care about the files installed all around your system, you just need to care about packages. IE: All system files, all applications, all run-able files, all libraries, all documentation and so forth is maintained by the package system. You should never have to deal with the files themselves directly. If you want to know which files a package installs, and where, simply query the RPM database for the list of files:
rpm --query --list <package name>