I had attempted to do the safari bookmark sync via iTunes and I ended up losing a bunch of iphone bookmarks, but I also got a couple of bonus bookmark folders that I could not delete... well more than one way to skin a cat.
If you are suffering from the same problem, or just want to clean house and remove all your bookmarks at once here a simple way. Load up your favorite iphoneinterface and grab your Bookmarks.plist file:
Make a copy of this file for backup purposes just encase you decide you didn't really want to delete your bookmarks.
I'm a PC user so I didn't have the luxury of being able to edit this file in its nice pretty xml format, if you are on a Mac you should be able to selectively edit this file as you wish.
I just opened the file in my text editor, did a select-all, delete, save.
Upload the file back to your iphone, and your safari bookmarks have a fresh start (and those pesky ones that didnít let you delete them are gone!).