I guess just three main reasons:
1) I am a very visual person, and like to see the project hierarchy. I like to click the file I want, instead of just using my keyboard. I know this flies in the face of the purist Emacs and Vim users, but I'm only about half hacker, and I like my clickey click.
2) I like the tabs at the top (as opposed to buffers that you can't see). I like to see the group of files I'm currently working with.
3) I like the Aptana plug-in, which does nice mark-up of HTML, Javascript, etc. It makes Eclipse a fairly nice web coding editor. I also like Pydev. So Eclipse supports all my favorite languages.
I do wish Eclipse were faster and stripped of many of its components. Also, I do use the command line for things like SVN and running commands in the terminal like "python manage.py runserver." But I like Eclipse as an editor.
Maybe it's just because Eclipse is what I'm used to. I suspect that is the root of all preference.