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No -- you aren't alone. Whenever I connect my daughter's iPhone to iTunes (say to add more music) we take our lives in our hands. You get scary popups that ask you a question and provides two options -- neither of which is what you want. I don't know whether this is deliberate on the part of Apple to discourage the use of iTunes, or whether they really think that it works well and is intuitive. For anybody from Apple…
Itunes is the worst. It can, without asking, delete the music from your device or your folders, reorganize your folders, rename your songs and reset their id3 tags. The mentality of "our users are stupid, just do everything for them" seems pervasive throughout apple's products.
If your user is stupid, they won't be able to manage a general purpose computer but will instead require a well-controlled computing appliance that will dutifully collect all the rents its creators can get away with.