That's kinda backwards- usually I hear people ask why they can't find a copy of iTunes which doesn't come with Quicktime. The reason for that is because the code which implements Apple's DRM mechanism is actually contained in the Quicktime libraries. They put it there so that Mac users will be able to play their protected files using players other than iTunes- on a Mac, any program which uses the Quicktime framework (i.e. shared library, much like a ".so" or ".dll" file) is able to play the protected files.
The same is true on Windows- their Quicktime player is able to play protected files which were purchased through the iTunes store (provided your computer is "authorized" for the account which purchased the file, of course.) My understanding (I don't write code for Windows) is that any other Windows program which use the Quicktime library can also play them.
The difference is that, on the Mac, the Quicktime framework is installed as a base part of the OS (much like IE on Windows) and therefore it's safe to assume it will always be there on a Mac. For Windows, it's not installed by default, and in fact can be removed by the user (after they uninstall iTunes, which won't work without it.)
As for why it installs Bonjour... first of all, it's not a system for locating other computers, it's a system for finding SERVICES on other computers. iTunes uses it to implement their "sharing" feature, where if multiple machines are running iTunes on the same network, they can play music from each others' libraries.
As for being able to install Quicktime without iTunes, I haven't tried in several years- my desktop and laptop machines are both Macs, and the only Windows machine I own anymore doesn't connect to the internet at all (I used it for ham radio, and install software using a USB stick) And because I'm using a Mac, Apple's web site only shows me the download links for the Mac, so I can't see what their offerings are for Windows.
As for why people use Quicktime to encode their videos "for whatever reason"... If a Windows user makes a video and distributes it, chances are it will be a ".wmv" file. Why? Because "Windows Media" support is built into the operating system, just as Quicktime is built into Mac OS X. Most users don't know, or care, about video codecs, container formats, or anything like that- all they know is that when they hit "go", it makes a file which they can play by double-clicking on it. Mac users are just as human as Windows users, and have the same "laziness" factor. When a Mac user doesn't tell their software any different, they end up producing Quicktime files. However, most of the newer programs are starting to default to MP4 files, which can be played by just about anything- which cannot be said of ".wmv" files.