Well I have to say that I've been using OS X so long that I've become quite acostomed to this behavior...
...but the more I think about it the more I totally agree with thendis. If it truely is the users documents, then nothing else should ever be put there.
Currently this folder has a ton of stuff I did not put there and also beleive belong in ~/Library/Application Support:
- Acrobat User Data
- AppleWorks User Data
- iChats
- Maxprog
- MCPref
- Microsoft User Data
- Microsoft User Data.old
- Mozilla
- NewRootApplet.java
- Office Projects
- Palm
- Retrospect_backup_schedules
- Virtual PC
- Virtual PC List
- Virtual PC Scripts