There are ways around the iTunes thing. iTunes has lossless capabilities, they have their own file type called Apple Lossless (ALAC - it's just a FLAC file with a different header). There are many converters out there that will quickly change FLAC to ALAC and then you can use them in iTunes like any other file.
If you are using a Mac, there are also numerous players that support FLAC, including Vox (my favorite), Cog, Songbird and others.
You can also use a program like 'FLUKE" which tricks iTunes into thinking the Flac file is a wav file, this allows you to keep the file in Flac format but still use iTunes.