Usually FLAC files are only made available for purchase/download from certain artists' own web sites. Examples of a couple artists selling certain albums and live shows in FLAC format include Dave Matthews Band and Phish. There are others, of course.
There are some useful links to things like this that you can find by frequenting the FLAC homepage ( http://flac.sf.net
No, the iTMS does not sell FLACs, but if you follow the latest news from Apple, they will be selling their EMI catalog in DRM-free AAC format at 256kbps. Perhaps in the future, an even wider range of higher quality DRM-free AAC files will be made available.
EDIT: So save some poking around on the FLAC homepage, click here
for a nice listing of lots of things available for sale/download in FLAC format.