I tried using Linux alternatives to iTunes, but it was always a pain. Even iTunes itself on a separate windows box was more of a hassle than I wanted. I eventually discovered rockbox, which works great with my iPod (5th gen AKA video): it has way more config options and allows me to simply create .m3u playlists and use my own folder structure. If your iPod is supported (https://www.rockbox.org/wiki/IpodPort.html), I’d absolutely recommend Rockbox over other solutions.

If your iPod isn’t supported by Rockbox (like my nano 5th gen), you could probably use strawberry or GTKpod. Both are imperfect, but work “good enough”.