Yeah, I had the same heartburn with iphoto years ago. I was still in the mindset of wanting to do file management myself. Now I'm buying in to the principle of letting the app manage the files in a DB. Or just generally taking file management away from user, but no one has really cracked the nut of how to that across multiple services and multiple devices.
You really do have to get over that psychological block about managing files to enjoy using iPhoto and Aperture.
Personally, I don't mind it, because it's one less thing to think about. I would prefer to buy a bigger drive than to worry about the placement of my photo files beyond the iPhoto/Aperture library package.
On the other hand, I know people with that file management mentality that hate, hate, hate iPhoto and Aperture's way of doing things.
