An aside question; what's the deal with "pathogen"?
I've been using the "/bin/cp" command for years installing vim plugins and it's worked remarkably well; requiring just about 1 invocation on average...
If you decide you no longer want a particular plugin, or want to upgrade it, it can be hard to tease out the files you /bin/cp'd into place. Adding a single folder under bundle makes removal easier later.
ETA: also note that git-cloning into bundle means that upgrading is just a question of entering the plugin directory and running git pull.
Each plugin resides in it's own directory, rather than being scattered around your .vim dir. Try to remove one of your installed plugins, you'll have to dig around and it'll be messy.
Also it makes it easier to update, since all you need to do is replace the folder with the newer version and you're all set.
To elaborate on the response others have offered about everything being in one folder, I'll further note that it allows you to keep track of the plugin through git, so you can very easily grab updates when desired.
Why git? I store my .vim directory in dropbox and just have it symlinked into my home directory on each of my machines. I don't really see a need for version control, and I don't want to have to do anything to make sure a change on one machine is reflected on all the others.
It lets you put your various vim things inside a single 'bundle' directory instead of having files in plugin/ftplugin and whatnot. Very convenient and easy to setup.
I've been using the "/bin/cp" command for years installing vim plugins and it's worked remarkably well; requiring just about 1 invocation on average...
What problem does that thing solve?