The reason iPhoto exists is so that you can work with your photos and not have to worry about the file structure. I have never even looked inside my iPhoto Library folder since I started using it.
Everything you could want to do with photos you can do from iPhoto in an easier way than rooting around in folders. These include:
- Managing in albums, smart albums, slideshows, calendars etc.
- Editing, either simply through iPhoto or by enabling the preferences to edit through professional programs such as Photoshop.
- Emailing, either by selecting the photos and hitting the "Email" button or dragging the photos into the Mail message.
- Burning back-up discs with album info and data all intact so that a HDD disaster doesn't wipe out all you albums and preferences.
- Printing
- Creative stuff with cards, postcards, calendars etc.
- Choose a single photo, an album or a bunch of photos randomly and hit the "Desktop" button, it will open System Preferences and let you set the change time etc to rotate your selected photos as your wallpaper.
- Access shared photos online, you can use iPhoto for Flickr RSS feeds as well as .Mac photocasts.
- Turning slideshows into movies.
The possibilities are endless and you don't ever have to open the iPhoto Library.
If you're absolutely paranoid about how you arrange your folders, you can enable a preference in iPhoto '06 to use your folder structure, it works exactly the same but doesn't auto arrange your photos. I can't be stuffed worrying about naming and placing folders, I just make sure I name the film roll something informative when I import the images and that way when I scroll in the iPhoto library I have a description of the roll flash up on screen as I go.