Tell itunes you want to manage the library yourself. Otherwise it will find every media file on the computer and start moving them to the location iTunes thinks is best but DAWs might not.
Then connect the iWhatever-it-is and tick the "manually manage/sync music and videos" box. After which you get to select what is transferred by iTunes,
No problem copying what I want on and off iPads or Mrs TLW's iPhone either, using iTunes in Windows or OS X. iTunes is like most software written with the lowest common denominator computer user in mind, it just needs firmly taking in hand from the start then checking it hasn't tried to get out of control again when updated. And at least you can control it, you just need to dig into the preferences.
Many of the people who attack iTunes do so I think because every time it gets updated the user interface changes. Messing around with GUIs for iTunes and iOS is Apple's (and a few other app publisher's) most annoying habit. Just because the app writer has fixed a few bugs or added/removed a minor feature doesn't mean I want to re-learn their software from scratch every three months.
Ripped CDs (use Apple lossless as the encoding system) work fine in iTunes by the way, and they can be transferred to iOS devices like any other audio. Me, I prefer it to any media player Microsoft has come up with, and unlike the Windows Media Player you don't have to pay extra for the Wondows Media Centre to get all the functions that should be there from the start.
Now, if only someone could come up with a DVD playing application that could actually handle the stupidly over the top security requirements to play protected Blu-Ray disks.....