I also don't like iTunes very much. But the problem with wanting to play FLAC on your iPod is that the iPod retail OS just won't do it, no matter what content management program you use.
One option for you is to install RockBox on your iPod. It supports a ton of different audio formats, including ogg and FLAC. It's still very early in development, but you can count on it getting better. Plus, it has a very nice support forum. I had it installed for a little while, and while it took a little while to learn how to use, and wasn't as intuitive as the retail OS, it was OK. Plus, with Rockbox, you don't need a program to put songs on your iPod - you just open it up like a harddrive in explorer, and copy the songs over. It automatically scans your file tree, and reads all the ID3 tags.
If you have an older iPod, you could also install linux, but this is usually more trouble than its worth. You can still install linux on the 5G, but they don't have music support yet. They do have some cool games though, and I've whiled away quite a few of my college classes playing minesweeper.
If you just want a program besides iTunes to put mp3, aac, ect files on your iPod, then there are a few options. Winamp has added support for portable players, including the ipod. Plus, Winamp is a great player, and has all the functions that iTunes is missing.
I know that there are more options, but these are the ones that I've tried personally. A google search of "iTunes Alternatives iPod" came up with quite a few ideas, even some that allow you to sync using WMP10 (Though why anyone would use WMP for music is beyond me).
Hope some of this helps. Oh, by the way, all these solutions are for PC, which is all that I have.